Package Onemap': February 17, 2020

Package ‘onemap’
February 17, 2020

Title Construction of Genetic Maps in Experimental Crosses: Full-Sib,
RILs, F2 and Backcrosses
Version 2.1.3
Description Analysis of molecular marker data from model (backcrosses,
F2 and recombinant inbred lines) and non-model systems (i. e.
outcrossing species). For the later, it allows statistical
analysis by simultaneously estimating linkage and linkage
phases (genetic map construction) according to Wu et al. (2002)
<doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint
approaches using hidden Markov models.
Date 2020-02-14
Author Gabriel Margarido [aut],
Marcelo Mollinari [aut],
Karl Broman [ctb],
Getulio Ferreira [ctb],
Rodrigo Amadeu [ctb],
Cristiane Taniguti [ctb, cre],
Augusto Garcia [aut, ctb]
LinkingTo Rcpp (>= 0.10.5)
Depends R (>= 3.6.0)
Imports ggplot2 (>= 2.2.1), plotly (>= 4.7.1), reshape2 (>= 1.4.1),
Rcpp (>= 0.10.5), graphics, methods, stats, utils, grDevices,
MDSMap
Suggests qtl (>= 1.36-6), knitr (>= 1.10), rmarkdown, htmlwidgets,
vcfR (>= 1.6.0),
VignetteBuilder knitr
Encoding UTF-8
License GPL-3
URL https://github.com/augusto-garcia/onemap
BugReports https://github.com/augusto-garcia/onemap/wiki
Maintainer Cristiane Taniguti <chtaniguti@usp.br>
1
2 R topics documented:
Repository CRAN
NeedsCompilation yes
Date/Publication 2020-02-17 06:00:04 UTC
RoxygenNote 7.0.2
biocViews
R topics documented:
add_marker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Bonferroni_alpha . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
combine_onemap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
compare . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
create_dataframe_for_plot_outcross . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
create_data_bins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
draw_map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
draw_map2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
drop_marker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
find_bins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
group_seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
make_seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
mapmaker_example_bc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
mapmaker_example_f2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
map_func . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
marker_type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
mds_onemap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
onemap_example_bc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
onemap_example_f2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
onemap_example_out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
onemap_example_riself . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
onemap_read_vcfR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
order_seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
plot.onemap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
plot.onemap_segreg_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
plot_by_segreg_type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
print.onemap_segreg_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
rcd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
read_mapmaker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
read_onemap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
rf_2pts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
rf_graph_table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
ripple_seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
select_segreg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
seriation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
add_marker 3
set_map_fun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
suggest_lod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
test_segregation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
test_segregation_of_a_marker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
try_seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
ug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
vcf2raw . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
vcf_example_bc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
vcf_example_f2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
vcf_example_out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
vcf_example_riself . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
write_map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
write_onemap_raw . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Index 70
add_marker Creates a new sequence by adding markers.
Description
Creates a new sequence by adding markers from a predetermined one. The markers are added in
the end of the sequence.
Usage
add_marker(input.seq, mrks)
Arguments
input.seq an object of class sequence.
mrks a vector containing the markers to be added from the sequence.
Value
An object of class sequence, which is a list containing the following components:
seq.num a vector containing the (ordered) indices of markers in the sequence, according
to the input file.
seq.phases a vector with the linkage phases between markers in the sequence, in corre-
sponding positions. -1 means that there are no defined linkage phases.
seq.rf a vector with the recombination fractions between markers in the sequence. -1
means that there are no estimated recombination fractions.
seq.like log-likelihood of the corresponding linkage map.
data.name name of the object of class onemap with the raw data.
twopt name of the object of class rf_2pts with the 2-point analyses.
@author Marcelo Mollinari, <mmollina@usp.br>

4 Bonferroni_alpha
See Also
drop_marker
Examples
data(onemap_example_out)
twopt <- rf_2pts(onemap_example_out)
all_mark <- make_seq(twopt,"all")
groups <- group(all_mark)
(LG1 <- make_seq(groups,1))
(LG.aug<-add_marker(LG1, c(4,7)))
Bonferroni_alpha Calculates individual significance level to be used to achieve a global

alpha (with Bonferroni)
Description
It shows the alpha value to be used in each chi-square segregation test, in order to achieve a given
global type I error. To do so, it uses Bonferroni’s criteria.
Usage
Bonferroni_alpha(x, global.alpha = 0.05)
Arguments
x an object of class onemap_segreg_test

global.alpha the global alpha that
Value
the alpha value for each test (numeric)
Examples
data(onemap_example_bc) # Loads a fake backcross dataset installed with onemap
Chi <- test_segregation(onemap_example_bc) # Performs the chi-square test for all markers
print(Chi) # Shows the results of the Chi-square tests
Bonferroni_alpha (Chi) # Shows the individual alpha level to be used
combine_onemap 5
combine_onemap Combine OneMap datasets
Description
Merge two or more OneMap datasets from the same cross type. Creates an object of class onemap.
Usage
combine_onemap(...)
Arguments
... Two or more onemap dataset objects of the same cross type.
Details
Given a set of OneMap datasets, all from the same cross type (full-sib, backcross, F2 intercross or
recombinant inbred lines obtained by self- or sib-mating), merges marker and phenotype informa-
tion to create a single onemap object.
If sample IDs are present in all datasets (the standard new format), not all individuals need to be
genotyped in all datasets - the merged dataset will contain all available information, with missing
data elsewhere. If sample IDs are missing in at least one dataset, it is required that all datasets have
the same number of individuals, and it is assumed that they are arranged in the same order in every
dataset.
Value
An object of class onemap, i.e., a list with the following components:
geno a matrix with integers indicating the genotypes read for each marker. Each col-
umn contains data for a marker and each row represents an individual.
n.ind number of individuals.
n.mar number of markers.
segr.type a vector with the segregation type of each marker, as strings.
segr.type.num a vector with the segregation type of each marker, represented in a simplified
manner as integers, i.e. 1 corresponds to markers of type "A"; 2 corresponds
to markers of type "B1.5"; 3 corresponds to markers of type "B2.6"; 4 corre-
sponds to markers of type "B3.7"; 5 corresponds to markers of type "C.8"; 6
corresponds to markers of type "D1" and 7 corresponds to markers of type "D2".
Markers for F2 intercrosses are coded as 1; all other crosses are left as NA.
input a string indicating that this is a combined dataset.
n.phe number of phenotypes.
pheno a matrix with phenotypic values. Each column contains data for a trait and each
row represents an individual.
6 compare
Author(s)
Gabriel R A Margarido, <gramarga@gmail.com>
References
Lincoln, S. E., Daly, M. J. and Lander, E. S. (1993) Constructing genetic linkage maps with MAP-
MAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical
Research Technical Report.
Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation
of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.
See Also
read_onemap and read_mapmaker.
Examples
## Not run:
combined_data <- combine_onemap(onemap_data1, onemap_data2)
## End(Not run)
compare Compare all possible orders (exhaustive search) for a given sequence
of markers
Description
n!
For a given sequence with n markers, computes the multipoint likelihood of all 2 possible orders.
Usage
compare(input.seq, n.best = 50, tol = 0.001, verbose = FALSE)
Arguments

n.best the number of best orders to store in object (defaults to 50).
tol tolerance for the C routine, i.e., the value used to evaluate convergence.
verbose if FALSE (default), simplified output is displayed. if TRUE, detailed output is
displayed.
compare 7
Details
Since the number n!2 is large even for moderate values of n, this function is to be used only for se-
quences with relatively few markers. If markers were genotyped in an outcross population, linkage
phases need to be estimated and therefore more states need to be visited in the Markov chain; when
segregation types are D1, D2 and C, computation can required a very long time (specially when
markers linked in repulsion are involved), so we recomend to use this function up to 6 or 7 markers.
For inbred-based populations, up to 10 or 11 markers can be ordered with this function, since link-
age phase are known. The multipoint likelihood is calculated according to Wu et al. (2002b) (Eqs.
7a to 11), assuming that the recombination fraction is the same in both parents. Hidden Markov
chain codes adapted from Broman et al. (2008) were used.
Value
An object of class compare, which is a list containing the following components:
best.ord a matrix containing the best orders.
best.ord.rf a matrix with recombination frequencies for the corresponding best orders.
best.ord.phase a matrix with linkage phases for the best orders.
best.ord.like a vector with log-likelihood values for the best orders.
best.ord.LOD a vector with LOD Score values for the best orders.
Author(s)
Marcelo Mollinari, <mmollina@usp.br>
References
Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL
experiments R package version 1.09-43
Jiang, C. and Zeng, Z.-B. (1997). Mapping quantitative trait loci with dominant and missing mark-
ers in various crosses from two inbred lines. Genetica 101: 47-58.
Lander, E. S., Green, P., Abrahamson, J., Barlow, A., Daly, M. J., Lincoln, S. E. and Newburg, L.
(1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage
maps of experimental and natural populations. Genomics 1: 174-181.
Mollinari, M., Margarido, G. R. A., Vencovsky, R. and Garcia, A. A. F. (2009) Evaluation of algo-
rithms used to order markers on genetics maps. _Heredity_ 103: 494-502.
Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002a) Simultaneous maximum likelihood esti-
mation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61:
349-363.
Wu, R., Ma, C.-X., Wu, S. S. and Zeng, Z.-B. (2002b). Linkage mapping of sex-specific differences.
Genetical Research 79: 85-96
See Also
marker_type for details about segregation types and make_seq.
8 create_dataframe_for_plot_outcross
Examples
## Not run:
#outcrossing example
markers <- make_seq(twopt,c(12,14,15,26,28))
(markers.comp <- compare(markers))
(markers.comp <- compare(markers,verbose=TRUE))
#F2 example
data(onemap_example_f2)
twopt <- rf_2pts(onemap_example_f2)
markers <- make_seq(twopt,c(17,26,29,30,44,46,55))
(markers.comp <- compare(markers))
(markers.comp <- compare(markers,verbose=TRUE))
## End(Not run)
create_dataframe_for_plot_outcross
Create a dataframe suitable for a ggplot2 graphic
Description
An internal function that prepares a dataframe suitable for drawing a graphic of raw data using
ggplot2, i. e., a data frame with long format
Usage
create_dataframe_for_plot_outcross(x)
Arguments
x an object of classes onemap and outcross, with data and additional information
Value
a dataframe
create_data_bins 9
create_data_bins New dataset based on bins
Description
Creates a new dataset based on onemap_bin object
Usage
create_data_bins(input.obj, bins)
Arguments
input.obj an object of class onemap.

bins an object of class onemap_bin.
Details
Given a onemap_bin object, creates a new data set where the redundant markers are collapsed into
bins and represented by the marker with the lower amount of missing data among those on the bin.
Value
an object of class onemap.
Author(s)
See Also
find_bins
Examples
## Not run:
load(url("https://github.com/mmollina/data/raw/master/fake_big_data_f2.RData"))
fake.big.data.f2
(bins <- find_bins(fake.big.data.f2, exact=FALSE))
(new.data <- create_data_bins(fake.big.data.f2, bins))
## End(Not run)
10 draw_map
draw_map Draw a genetic map
Description
Provides a simple draw of a genetic map.
Usage
draw_map(
map.list,
horizontal = FALSE,
names = FALSE,
grid = FALSE,
cex.mrk = 1,
cex.grp = 0.75
)
Arguments
map.list a map, i.e. an object of class sequence with a predefined order, linkage phases,
recombination fraction and likelihood; also it could be a list of maps.
horizontal if TRUE, indicates that the map should be plotted horizontally. Default is FALSE
names if TRUE, displays the names of the markers. Default is FALSE
grid if TRUE, displays a grid in the background. Default is FALSE
cex.mrk the magnification to be used for markers.
cex.grp the magnification to be used for group axis annotation.
Author(s)
Examples
## Not run:
#outcross example
lg<-group(make_seq(twopt, "all"))
maps<-vector("list", lg$n.groups)
for(i in 1:lg$n.groups)
maps[[i]]<- make_seq(order_seq(input.seq= make_seq(lg,i),twopt.alg =
"rcd"), "force")
draw_map(maps, grid=TRUE)
draw_map(maps, grid=TRUE, horizontal=TRUE)
draw_map2 11
#F2 example
twopt<-rf_2pts(onemap_example_f2)
maps<-vector("list", lg$n.groups)
for(i in 1:lg$n.groups)
maps[[i]]<- make_seq(order_seq(input.seq= make_seq(lg,i),twopt.alg =
"rcd"), "force")
draw_map(maps, grid=TRUE)
draw_map(maps, grid=TRUE, horizontal=TRUE)
## End(Not run)
draw_map2 Draw a linkage map
Description
Provides a simple draw of a linkage map.
Usage
draw_map2(
...,
tag = NULL,
id = TRUE,
pos = TRUE,
cex.label = NULL,
main = NULL,
group.names = NULL,
centered = F,
y.axis = TRUE,
space = NULL,
col.group = NULL,
col.mark = NULL,
col.tag = NULL,
output = NULL
)
Arguments
... map(s). Object(s) of class sequence and/or data.frame. If data.frame, it
must have two columns: column 1: marker id; column 2: position (cM) (numeric).
tag name(s) of the marker(s) to highlight. If "all", all markers will be highlighted.
Default is NULL.
id logical. If TRUE (default), shows name(s) of tagged marker(s).
12 draw_map2
pos logical. If TRUE (default), shows position(s) of tagged marker(s).

cex.label the magnification used for label(s) of tagged marker(s). If NULL (default), the
cex will be automatically calculated to avoid overlapping.
main an overall title for the plot. Default is NULL.
group.names name(s) to identfy the group(s). If NULL (default), the name(s) of the sequence(s)
will be used.
centered logical. If TRUE, the group(s) will be aligned in the center. If FALSE (default),
the group(s) will be aligned at the top.
y.axis logical. If TRUE (default), shows y axis. If centered = TRUE, the y axis will
always be hidden.
space numerical. Spacing between groups. If NULL (default), the spacing will be auto-
matically calculated to avoid overlapping.
col.group the color used for group(s).
col.mark the color used for marker(s).
col.tag the color used for highlighted marker(s) and its/theirs label(s).
output the name of the output file. The file format can be specified by adding its exten-
sion. Available formats: ’bmp’, ’jpeg’, ’png’, ’tiff’, ’pdf’ and ’eps’ (default).
Author(s)
Getulio Caixeta Ferreira, <getulio.caifer@gmail.com>
Examples
## Not run:
data("onemap_example_out")
seq1<-make_seq(order_seq(input.seq= make_seq(lg,1),twopt.alg = "rcd"), "force")
draw_map2(seq1,seq2,seq3,tag = c("M1","M2","M3","M4","M5"))
data("onemap_example_f2")
seq<-list(
make_seq(order_seq(input.seq= make_seq(lg,1),twopt.alg = "rcd"), "force"),
make_seq(order_seq(input.seq= make_seq(lg,2),twopt.alg = "rcd"), "force"),
make_seq(order_seq(input.seq= make_seq(lg,3),twopt.alg = "rcd"), "force")
)
draw_map2(seq,tag = "all",group.names = c("Chr 1","Chr 2","Chr 3"),main="Linkage Map")
## End(Not run)
drop_marker 13
drop_marker Creates a new sequence by dropping markers.
Description
Creates a new sequence by dropping markers from a predetermined one.
Usage
drop_marker(input.seq, mrks)
Arguments
mrks a vector containing the markers to be removed from the sequence.
Value
to the input file.
seq.rf a vector with the recombination fractions between markers in the sequence. -1
means that there are no estimated recombination fractions.
@author Marcelo Mollinari, <mmollina@usp.br>
See Also
add_marker
Examples
(LG1 <- make_seq(groups,1))
(LG.aug<-drop_marker(LG1, c(10,14)))
14 find_bins
find_bins Allocate markers into bins
Description
Function to allocate markers with redundant information into bins. Within each bin, the pairwise
recombination fraction between markers is zero.
Usage
find_bins(input.obj, exact = TRUE, ch = NULL)
Arguments

exact logical. If TRUE, it only allocates markers with the exact same information into
bins, including missing data; if FALSE, missing data are not considered when
allocating markers. In the latter case, the marker with the lowest amount of
missing data is taken as the representative marker on that bin.
ch not used in this OneMap version. Chromosome for which the analysis should
be performed. If NULL the analisys is performed for all chromosomes.
Value
An object of class onemap_bin, which is a list containing the following components:
bins a list containing the bins. Each element of the list is a table whose lines indicate
the name of the marker, the bin in which that particular marker was allocated and
the percentage of missing data. The name of each element of the list corresponds
to the marker with the lower amount of missing data among those on the bin
n.mar total number of markers.
n.ind number individuals
exact.search logical; indicates if the search was performed with the argument exact=TRUE or
exact=FALSE
Author(s)
See Also
create_data_bins
group 15
Examples
## Not run:
load(url("https://github.com/mmollina/data/raw/master/fake_big_data_f2.RData"))
fake.big.data.f2
(bins<-find_bins(fake.big.data.f2, exact=FALSE))
## End(Not run)
group Assign markers to linkage groups
Description
Identifies linkage groups of markers, using results from two-point (pairwise) analysis and the tran-
sitive property of linkage.
Usage
group(input.seq, LOD = NULL, max.rf = NULL, verbose = TRUE)
Arguments
LOD a (positive) real number used as minimum LOD score (threshold) to declare
linkage.
max.rf a real number (usually smaller than 0.5) used as maximum recombination frac-
tion to declare linkage.
verbose logical. If TRUE, current progress is shown; if FALSE, no output is produced.
Details
If the arguments specifying thresholds used to group markers, i.e., minimum LOD Score and max-
imum recombination fraction, are NULL (default), the values used are those contained in object
input.seq. If not using NULL, the new values override the ones in object input.seq.
Value
Returns an object of class group, which is a list containing the following components:
data.name name of the object of class onemap that contains the raw data.
twopt name of the object of class rf.2ts used as input, i.e., containing information
used to assign markers to linkage groups.
marnames marker names, according to the input file.
LOD minimum LOD Score to declare linkage.
max.rf maximum recombination fraction to declare linkage.
n.groups number of linkage groups found.
groups number of the linkage group to which each marker is assigned.
16 group_seq
Author(s)
Gabriel R A Margarido, <gramarga@gmail.com> and Marcelo Mollinari, <mmollina@usp.br>
References
See Also
rf_2pts and make_seq
Examples
twopts <- rf_2pts(onemap_example_out)
all.data <- make_seq(twopts,"all")

link_gr <- group(all.data)
link_gr
print(link_gr, details=FALSE) #omit the names of the markers
group_seq Assign markers to preexisting linkage groups
Description
Identifies linkage groups of markers combining input sequences objects with unlinked markers
from rf_2pts object. The results from two-point (pairwise) analysis and the transitive property of
linkage are used for grouping, as group function.
Usage
group_seq(
input.2pts,
seqs = "CHROM",
unlink.mks = "all",
repeated = FALSE,
LOD = NULL,
max.rf = NULL
)
group_seq 17
Arguments
input.2pts an object of class rf_2pts.
seqs a list of objects of class sequence or the string "CHROM" if there is CHROM
information available in the input data file.
unlink.mks a object of class sequence with the number of the markers to be grouped with
the preexisting sequences defined by seqs parameter. Using the string "all", all
remaining markers of the rf_2pts object will be tested.
repeated logical. If TRUE, markers grouped in more than one of the sequences are keeped
in the output sequences. If FALSE, they are removed of the output sequences.
LOD a (positive) real number used as minimum LOD score (threshold) to declare
linkage.
max.rf a real number (usually smaller than 0.5) used as maximum recombination frac-
tion to declare linkage.
Details
If the arguments specifying thresholds used to group markers, i.e., minimum LOD Score and max-
imum recombination fraction, are NULL (default), the values used are those contained in object
input.2pts. If not using NULL, the new values override the ones in object input.2pts.
Value
Returns an object of class group_seq, which is a list containing the following components:
data.name name of the object of class onemap that contains the raw data.
twopt name of the object of class rf.2ts used as input, i.e., containing information
used to assign markers to linkage groups.
mk.names marker names, according to the input file.
input.seqs list with the numbers of the markers in each inputted sequence
input.unlink.mks
numbers of the unlinked markers in inputted sequence
out.seqs list with the numbers of the markers in each outputted sequence
n.unlinked number of markers that remained unlinked
n.repeated number of markers which repeated in more than one group
n.mar total number of markers evaluated
sequences list of outputted sequences
repeated list with the number of the markers that are repeated in each outputted sequence
unlinked number of the markers which remained unlinked
Author(s)
Cristiane Taniguti, <chtaniguti@usp.br>
18 make_seq
See Also
make_seq and group
Examples
data(onemap_example_out) # load OneMap's fake dataset for a outcrossing population
data(vcf_example_out) # load OneMap's fake dataset from a VCF file for a outcrossing population
comb_example <- combine_onemap(onemap_example_out, vcf_example_out) # Combine datasets
twopts <- rf_2pts(comb_example)
out_CHROM <- group_seq(twopts, seqs="CHROM", repeated=FALSE)

out_CHROM
seq1 <- make_seq(twopts, c(1,2,3,4,5,25,26))

seq2 <- make_seq(twopts, c(8,18))
seq3 <- make_seq(twopts, c(4,16,20,21,24,29))
out_seqs <- group_seq(twopts, seqs=list(seq1,seq2,seq3))

out_seqs
make_seq Create a sequence of markers
Description
Makes a sequence of markers based on an object of another type.
Usage
make_seq(input.obj, arg = NULL, phase = NULL, data.name = NULL, twopt = NULL)
Arguments
input.obj an object of class onemap, rf_2pts, group, compare, try or order.
arg its value depends on the type of object input.obj. For a onemap object, arg
must be a string corresponding to one of the reference sequences on which mark-
ers are anchored (usually chromosomes). This requires that CHROM information
be available in the input data file. It can also be a vector of integers specifying
which markers comprise the sequence. For an object rf_2pts, arg can be the
string "all", resulting in a sequence with all markers in the raw data (generally
done for grouping markers); otherwise, it must be a vector of integers speci-
fying which markers comprise the sequence. For an object of class group, arg
must be an integer specifying the group. For a compare object, arg is an inte-
ger indicating the corresponding order (arranged according to the likelihood);
if NULL (default), the best order is taken. For an object of class try, arg must
be an integer less than or equal to the length of the original sequence plus one;
make_seq 19
the sequence obtained will be that with the additional marker in the position in-
dicated by arg. Finally, for an order object, arg is a string: "safe" means the
order that contains only markers mapped with the provided threshold; "force"
means the order with all markers.
phase its value is also dependent on the type of input.obj. For an rf_2pts or onemap
object, phase can be a vector with user- defined linkage phases (its length is
equal to the number of markers minus one); if NULL (default), other functions
will try to find the best linkage phases. For example, if phase takes on the
vector c(1,2,3,4), the sequence of linkage phases will be coupling/coupling,
coupling/repulsion, repulsion/coupling and repulsion/repulsion for a sequence
of five markers. If input.obj is of class compare or try, this argument indi-
cates which combination of linkage phases should be chosen, for the particular
order given by argument arg. In both cases, NULL (default) makes the best com-
bination to be taken. If input.obj is of class, group or order, this argument
has no effect.
data.name a string indicating the name of the object which contains the raw data. This
does not have to be defined by the user: it is here for compatibility issues when
calling make_seq from inside other functions.
twopt a string indicating the name of the object which contains the two-point infor-
mation. This does not have to be defined by the user: it is here for compatibility
issues when calling make_seq from inside other functions.
Value
to the input file.
seq.rf a vector with the recombination frequencies between markers in the sequence.
-1 means that there are no estimated recombination frequencies.
Author(s)
Gabriel Margarido, <gramarga@gmail.com>
References
20 map
See Also
compare, try_seq, order_seq and map.
Examples
## Not run:

all_mark <- make_seq(twopt,1:30) # same as above, for this data set
LG1 <- make_seq(groups,1)
LG1.ord <- order_seq(LG1)
(LG1.final <- make_seq(LG1.ord)) # safe order
(LG1.final.all <- make_seq(LG1.ord,"force")) # forced order
markers <- make_seq(twopt,c(2,3,12,14))

markers.comp <- compare(markers)
(base.map <- make_seq(markers.comp))
base.map <- make_seq(markers.comp,1,1) # same as above
(extend.map <- try_seq(base.map,30))
(base.map <- make_seq(extend.map,5)) # fifth position is the best
## End(Not run)
map Construct the linkage map for a sequence of markers
Description
Estimates the multipoint log-likelihood, linkage phases and recombination frequencies for a se-
quence of markers in a given order.
Usage
map(input.seq, tol = 1e-04, verbose = FALSE, mds.seq = FALSE)
Arguments
verbose If TRUE, print tracing information.
mds.seq When some pair of markers do not follow the linkage criteria, if TRUE one of the
markers is removed and returns a vector with remaining marker numbers (useful
for mds_onemap function).
map 21
Details
Markers are mapped in the order defined in the object input.seq. If this object also contains
a user-defined combination of linkage phases, recombination frequencies and log-likelihood are
estimated for that particular case. Otherwise, the best linkage phase combination is also estimated.
The multipoint likelihood is calculated according to Wu et al. (2002b)(Eqs. 7a to 11), assuming
that the recombination fraction is the same in both parents. Hidden Markov chain codes adapted
from Broman et al. (2008) were used.
Value
to the input file.
Author(s)
Adapted from Karl Broman (package ’qtl’) by Gabriel R A Margarido, <gramarga@usp.br> and
Marcelo Mollinari, <mmollina@gmail.com>
References
349-363.
See Also
make_seq
22 mapmaker_example_bc
Examples
## Not run:
markers <- make_seq(twopt,c(30,12,3,14,2)) # correct phases

map(markers)
markers <- make_seq(twopt,c(30,12,3,14,2),phase=c(4,1,4,3)) # incorrect phases

map(markers)
## End(Not run)
mapmaker_example_bc Simulated data from a backcross population
Description
Simulated data set from a backcross population.
Usage
data(mapmaker_example_bc)
Format
The format is: List of 8 $ geno : num [1:150, 1:67] 1 2 1 1 2 1 2 1 1 2 ... ..- attr(*, "dimnames")=List
of 2 .. ..$ : NULL .. ..$ : chr [1:67] "M1" "M2" "M3" "M4" ... $ n.ind : num 150 $ n.mar : num 67
$ segr.type : chr [1:67] "A.H" "A.H" "A.H" "A.H" ... $ segr.type.num: logi [1:67] NA NA NA NA
NA NA ... $ input : chr "inst/extdata/mapmaker_example_bc.raw" $ n.phe : num 1 $ pheno : num
[1:150, 1] 40.8 39.5 37.9 34.2 38.9 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr
"Trait_1" - attr(*, "class")= chr [1:2] "onemap" "backcross"
Details
A total of 150 individuals were genotyped for 67 markers with 15% of missing data. There is one
quantitative phenotype to show how to use onemap output as R\qtl input.
Author(s)
See Also

mapmaker_example_f2 23
Examples
data(mapmaker_example_bc)
# perform two-point analyses

twopts <- rf_2pts(mapmaker_example_bc)
twopts
mapmaker_example_f2 Simulated data from a F2 population
Description
Simulated data set from a F2 population.
Usage
data("mapmaker_example_f2")
Format
of 2 .. ..$ : NULL .. ..$ : chr [1:66] "M1" "M2" "M3" "M4" ... $ n.ind : num 200 $ n.mar : num 66 $
segr.type : chr [1:66] "A.H.B" "C.A" "D.B" "C.A" ... $ segr.type.num: num [1:66] 1 3 2 3 3 2 1 3 2 1
... $ input : chr "/home/cristiane/R/x86_64-pc-linux-gnu-library/3.4/onemap/extdata/mapmaker_example_f2.raw"
$ n.phe : num 1 $ pheno : num [1:200, 1] 37.6 36.4 37.2 35.8 37.1 ... ..- attr(*, "dimnames")=List
of 2 .. ..$ : NULL .. ..$ : chr "Trait_1" - attr(*, "class")= chr [1:2] "onemap" "f2"
Details
A total of 200 individuals were genotyped for 66 markers (36 co-dominant, i.e. a, ab or b and 30
dominant i.e. c or a and d or b) with 15% of missing data. There is one quantitative phenotype
to show how to use onemap output as R\qtl and QTL Cartographer input. Also, it is used for the
analysis in the tutorial that comes with OneMap.
Examples
data(mapmaker_example_f2)

twopts <- rf_2pts(mapmaker_example_f2)
twopts
24 map_func
map_func Mapping functions Haldane and Kosambi
Description
Functions to convert recombination fractions to distance in cM (centiMorgans).
Usage
haldane(rcmb)
kosambi(rcmb)
Arguments
rcmb A recombination fraction between two markers, i.e., a number between 0 and
0.5.
Details
Haldane mapping function is defined as
1
dM = − ln(1 − 2r),
2
for 0 ≤ r ≤ 0.5, where r stands for the recombination fraction in rcmb. Kosambi mapping function
is
1 1 + 2r
dM = ln ,
4 1 − 2r
for 0 ≤ r ≤ 0.5, where r is defined as above.
Value
Both functions return a number with a distance measured in cM.
Author(s)
References
Haldane, J. B. S. (1919) The combination of linkage values and the calculation of distance between
the loci of linked factors. Journal of Genetics 8: 299-309.
Kosambi, D. D. (1944) The estimation of map distance from recombination values. Annuaire of
Eugenetics 12: 172-175.
marker_type 25
Examples
# little difference for small recombination fractions
haldane(0.05)
kosambi(0.05)
# greater difference as recombination fraction increases

haldane(0.35)
kosambi(0.35)
marker_type Informs the segregation patterns of markers
Description
Informs the type of segregation of all markers from an object of class sequence. For outcross
populations it uses the notation by Wu et al., 2002. For backcrosses, F2s and RILs, it uses the
traditional notation from MAPMAKER i.e. AA, AB, BB, not AA and not BB.
Usage
marker_type(input.seq)
Arguments
Details
The segregation types are (Wu et al., 2002 ):
Type Cross Segregation

A.1 ab x cd 1:1:1:1
A.2 ab x ac 1:1:1:1
A.3 ab x co 1:1:1:1
A.4 ao x bo 1:1:1:1
B1.5 ab x ao 1:2:1
B2.6 ao x ab 1:2:1
B3.7 ab x ab 1:2:1
C8 ao x ao 3:1
D1.9 ab x cc 1:1
D1.10 ab x aa 1:1
D1.11 ab x oo 1:1
D1.12 bo x aa 1:1
D1.13 ao x oo 1:1
D2.14 cc x ab 1:1
D2.15 aa x ab 1:1
D2.16 oo x ab 1:1
D2.17 aa x bo 1:1
D2.18 oo x ao 1:1
26 mds_onemap
Value
Nothing is returned. Segregation types of all markers in the sequence are displayed on the screen.
Author(s)
References
See Also
make_seq
Examples
markers.ex <- make_seq(twopts,c(3,6,8,12,16,25))
marker_type(markers.ex) # segregation type for some markers
twopts <- rf_2pts(onemap_example_f2)
all_mrk<-make_seq(twopts, "all")
lgs<-group(all_mrk)
lg1<-make_seq(lgs,1)
marker_type(lg1) # segregation type for linkage group 1
mds_onemap OneMap interface with MDSMap package with possibilitie of multi-

point distances estimation
Description
For a given sequence of markers, apply mds method described in Preedy and Hackett (2016) using
MDSMap package to ordering markers and estimates the genetic distances with OneMap multipoint
approach. Also gives MDSMap input file format for directly analysis in this package.
Usage
mds_onemap(
input.seq,
out.file = "out.file",
mds.graph.file = "NULL.pdf",
mds_onemap 27
p = NULL,
n = NULL,
ispc = TRUE,
displaytext = FALSE,
weightfn = "lod2",
mapfn = "haldane",
hmm = TRUE,
mds.seq = TRUE
)
Arguments
input.seq an object of class sequence
out.file path to the generated MDSMap input file.
mds.graph.file path to the graphic generated by MDSMap
p Integer - the penalty for deviations from the sphere - higher p forces points more
closely onto a sphere.
n Vector of integers or strings containing markers to be omitted from the analysis.
ispc Logical determining the method to be used to estimate the map. By default this
is TRUE and the method of principal curves will be used. If FALSE then the
constrained MDS method will be used.
displaytext Shows markers names in analysis graphic view
weightfn Character string specifying the values to use for the weight matrix in the MDS
’lod2’ or ’lod’.
mapfn Character string specifying the map function to use on the recombination frac-
tions ’haldane’ is default, ’kosambi’ or ’none’.
hmm Multipoint genetic distance estimation
mds.seq When some pair of markers do not follow the linkage criteria, if TRUE one of the
markers is removed and mds is performed again.
Details
For better description about MDS method, see MDSMap package vignette.
Value
to the input file.
28 onemap_example_bc
Author(s)
References
Preedy, K. F. and Hackett, C. A. (2016). A rapid marker ordering approach for high-density genetic
linkage maps in experimental autotetraploid populations using multidimensional scaling. Theoreti-
cal and Applied Genetics 129: 2117-2132
rithms used to order markers on genetics maps. Heredity 103: 494-502.
349-363.
See Also
https://CRAN.R-project.org/package=MDSMap.
onemap_example_bc Simulated data from a backcross population
Description
Simulated data set from a backcross population.
Usage
data(onemap_example_bc)
Format
of 2 .. ..$ : chr [1:150] "ID1" "ID2" "ID3" "ID4" ... .. ..$ : chr [1:67] "M1" "M2" "M3" "M4" ... $
n.ind : int 150 $ n.mar : int 67 $ segr.type : chr [1:67] "A.H" "A.H" "A.H" "A.H" ... $ segr.type.num:
logi [1:67] NA NA NA NA NA NA ... $ n.phe : int 1 $ pheno : num [1:150, 1] 40.8 39.5 37.9 34.2
38.9 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr "Trait_1" $ CHROM : NULL
$ POS : NULL $ input : chr "onemap_example_bc.raw" - attr(*, "class")= chr [1:2] "onemap"
"backcross"
Details
A total of 150 individuals were genotyped for 67 markers with 15% of missing data. There is one
quantitative phenotype to show how to use onemap output as R\qtl input.
onemap_example_f2 29
Author(s)
See Also
Examples

twopts <- rf_2pts(onemap_example_bc)
twopts
onemap_example_f2 Simulated data from a F2 population
Description
Simulated data set from a F2 population.
Usage
data("onemap_example_f2")
Format
The format is: List of 10 $ geno : num [1:200, 1:66] 1 3 2 2 1 0 3 1 1 3 ... ..- attr(*, "dim-
names")=List of 2 .. ..$ : chr [1:200] "IND1" "IND2" "IND3" "IND4" ... .. ..$ : chr [1:66] "M1"
"M2" "M3" "M4" ... $ n.ind : int 200 $ n.mar : int 66 $ segr.type : chr [1:66] "A.H.B" "C.A"
"D.B" "C.A" ... $ segr.type.num: num [1:66] 1 3 2 3 3 2 1 3 2 1 ... $ n.phe : int 1 $ pheno : num
[1:200, 1] 37.6 36.4 37.2 35.8 37.1 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr
"Trait_1" $ CHROM : NULL $ POS : NULL $ input : chr "/home/cristiane/R/x86_64-pc-linux-gnu-
library/3.4/onemap/extdata/onemap_example_f2.raw" - attr(*, "class")= chr [1:2] "onemap" "f2"
Details
A total of 200 individuals were genotyped for 66 markers (36 co-dominant, i.e. a, ab or b and 30
dominant i.e. c or a and d or b) with 15% of missing data. There is one quantitative phenotype
to show how to use onemap output as R\qtl and QTL Cartographer input. Also, it is used for the
analysis in the tutorial that comes with OneMap.
Examples
plot(onemap_example_f2)
30 onemap_example_out
onemap_example_out Data from a full-sib family derived from two outbred parents
Description
Simulated data set for an outcross, i.e., an F1 population obtained by crossing two non-homozygous
parents.
Usage
Format
An object of class onemap.
Details
A total of 100 F1 individuals were genotyped for 30 markers. The data currently contains only
genotype information (no phenotypes). It is included to be used as a reference in order to understand
how a data file needs to be. Also, it is used for the analysis in the tutorial that comes with OneMap.
Author(s)
See Also
read_onemap for details about objects of class onemap.
Examples

twopts
onemap_example_riself 31
onemap_example_riself Simulated data from a RIL population produced by selfing.
Description
Simulated biallelic data set for an ri self population.
Usage
data("onemap_example_riself")
Format
of 2 .. ..$ : chr [1:100] "ID1" "ID2" "ID3" "ID4" ... .. ..$ : chr [1:68] "M1" "M2" "M3" "M4" ... $
n.ind : int 100 $ n.mar : int 68 $ segr.type : chr [1:68] "A.B" "A.B" "A.B" "A.B" ... $ segr.type.num:
logi [1:68] NA NA NA NA NA NA ... $ n.phe : int 0 $ pheno : NULL $ CHROM : NULL $ POS :
NULL $ input : chr "onemap_example_riself.raw" - attr(*, "class")= chr [1:2] "onemap" "riself"
Details
A total of 100 F1 individuals were genotyped for 68 markers. The data currently contains only
genotype information (no phenotypes). It is included to be used as a reference in order to understand
how a data file needs to be.
Author(s)
See Also
Examples
data(onemap_example_riself)
plot(onemap_example_riself)
32 onemap_read_vcfR
onemap_read_vcfR Convert vcfR object to onemap object
Description
Converts data from a vcfR package to onemap initial object, while trying to identify the appropriate
marker segregation patterns.
Usage
onemap_read_vcfR(
vcfR.object = NULL,
cross = c("outcross", "f2 intercross", "f2 backcross", "ri self", "ri sib"),
parent1 = NULL,
parent2 = NULL
)
Arguments
vcfR.object object of class ’vcfR’ from vcfR package.
cross type of cross. Must be one of: "outcross" for full-sibs; "f2 intercross" for
an F2 intercross progeny; "f2 backcross"; "ri self" for recombinant inbred
lines by self-mating; or "ri sib" for recombinant inbred lines by sib-mating.
parent1 string specifying sample ID of the first parent.
parent2 string specifying sample ID of the second parent.
Details
Only biallelic SNPs and indels for diploid variant sites are considered.
Genotype information on the parents is required for all cross types. For full-sib progenies, both
outbred parents must be genotyped. For backcrosses, F2 intercrosses and recombinant inbred lines,
the original inbred lines must be genotyped. Particularly for backcross progenies, the recurrent line
must be provided as the first parent in the function arguments.
Marker type is determined based on parental genotypes. Variants for which parent genotypes cannot
be determined are discarded.
Reference sequence ID and position for each variant site are also stored.
Author(s)
See Also
read_onemap for a description of the output object of class onemap.
order_seq 33
Examples
## Not run:
vcfR.object <- vcfR::read.vcfR(system.file("extdata/vcf_example_out.vcf", package = "onemap"))
data <- onemap_read_vcfR(vcfR.object=vcfR.object,
cross="outcross",
parent1=c("P1"),
parent2=c("P2"))
## End(Not run)
order_seq Search for the best order of markers combining compare and try_seq
functions
Description
For a given sequence of markers, this function first uses the compare function to create a frame-
work for a subset of informative markers. Then, it tries to map remaining ones using the try_seq
function.
Usage
order_seq(
input.seq,
n.init = 5,
subset.search = c("twopt", "sample"),
subset.n.try = 30,
subset.THRES = 3,
twopt.alg = c("rec", "rcd", "ser", "ug"),
THRES = 3,
touchdown = FALSE,
tol = 0.1
)
Arguments
n.init the number of markers to be used in the compare step (defaults to 5).
subset.search a character string indicating which method should be used to search for a subset
of informative markers for the compare step. It is used for backcross, F2 or RIL
populations, but not for outcrosses. See the Details section.
subset.n.try integer. The number of times to repeat the subset search procedure. It is only
used if subset.search=="sample". See the Details section.
subset.THRES numerical. The threshold for the subset search procedure. It is only used if
subset.search=="sample". See the Details section.
34 order_seq
twopt.alg a character string indicating which two-point algorithm should be used if subset.search=="twopt".
See the Details section.
THRES threshold to be used when positioning markers in the try_seq step.
touchdown logical. If FALSE (default), the try_seq step is run only once, with the value of
THRES. If TRUE, try_seq runs with THRES and then once more, with THRES-1.
The latter calculations take longer, but usually are able to map more markers.
tol tolerance number for the C routine, i.e., the value used to evaluate convergence
of the EM algorithm.
Details
For outcrossing populations, the initial subset and the order in which remaining markers will be
used in the try_seq step is given by the degree of informativeness of markers (i.e markers of type
A, B, C and D, in this order).
For backcrosses, F2s or RILs, two methods can be used for choosing the initial subset: i) "sample"
randomly chooses a number of markers, indicated by n.init, and calculates the multipoint log-
likelihood of the n.init!
2 possible orders. If the LOD Score of the second best order is greater than
subset.THRES, than it takes the best order to proceed with the try_seq step. If not, the procedure
is repeated. The maximum number of times to repeat this procedure is given by the subset.n.try
argument. ii) "twopt" uses a two-point based algorithm, given by the option "twopt.alg", to
construct a two-point based map. The options are "rec" for RECORD algorithm, "rcd" for Rapid
Chain Delineation, "ser" for Seriation and "ug" for Unidirectional Growth. Then, equally spaced
markers are taken from this map. The "compare" step will then be applied on this subset of markers.
In both cases, the order in which the other markers will be used in the try_seq step is given by
marker types (i.e. co-dominant before dominant) and by the missing information on each marker.
After running the compare and try_seq steps, which result in a "safe" order, markers that could
not be mapped are "forced" into the map, resulting in a map with all markers positioned.
Value
An object of class order, which is a list containing the following components:
ord an object of class sequence containing the "safe" order.

mrk.unpos a vector with unpositioned markers (if they exist).
LOD.unpos a matrix with LOD-Scores for unmapped markers, if any, for each position in
the "safe" order.
THRES the same as the input value, just for printing.
ord.all an object of class sequence containing the "forced" order, i.e., the best order
with all markers.
Author(s)
Gabriel R A Margarido, <gramarga@usp.br> and Marcelo Mollinari, <mmollina@gmail.com>
order_seq 35
References
Lander, E. S. and Green, P. (1987). Construction of multilocus genetic linkage maps in humans.
Proc. Natl. Acad. Sci. USA 84: 2363-2367.
349-363.
See Also
make_seq, compare and try_seq.
Examples
## Not run:
#outcross example
LG2.ord <- order_seq(LG2,touchdown=TRUE)
LG2.ord
make_seq(LG2.ord) # get safe sequence
make_seq(LG2.ord,"force") # get forced sequence
#F2 example
LG3.ord <- order_seq(LG3, subset.search = "twopt", twopt.alg = "rcd", touchdown=TRUE)
LG3.ord
ord.1<-make_seq(LG3.ord,"force") # get forced sequence
LG3.ord.s <- order_seq(LG3, subset.search = "sample", touchdown=TRUE)

36 plot.onemap
LG3.ord.s
rbind(ord.1$seq.num, ord.2$seq.num) # probably, the same order for

this dataset
## End(Not run)
plot.onemap Draw a graphic of raw data for any OneMap population
Description
Shows a heatmap (in ggplot2, a graphic of geom "tile") for raw data. Lines correspond to mark-
ers and columns to individuals. The function can plot a graph for all marker types, depending
of the cross type (dominant/codominant markers, in all combinations). The function receives a
onemap object of class onemap, reads information from genotypes from this object, converts it
to a long dataframe format using function melt() from package reshape2() or internal function cre-
ate_dataframe_for_plot_outcross(), converts numbers from the object to genetic notation (according
to the cross type), then plots the graphic. If there is more than 20 markers, removes y labels For
outcross populations, it can show all markers together, or it can split them according the segregation
pattern.
Usage
## S3 method for class 'onemap'
plot(x, all = TRUE, ...)
Arguments
x an object of class onemap, with data and additional information
all a TRUE/FALSE option to indicate if results will be plotted together (if TRUE) or
splitted based on their segregation pattern. Only used for outcross populations.
... currently ignored
Value
a ggplot graphic
Examples
## Not run:
plot(onemap_example_bc) # This will show you the graph
# You can store the graphic in an object, then save it with a number of properties
plot.onemap_segreg_test 37
# For details, see the help of ggplot2's function ggsave()

g <- plot(onemap_example_bc)
ggplot2::ggsave("MyRawData_bc.jpg", g, width=7, height=4, dpi=600)
data(onemap_example_f2) # Loads a fake backcross dataset installed with onemap

plot(onemap_example_f2) # This will show you the graph
# You can store the graphic in an object, then save it with a number of properties
g <- plot(onemap_example_f2)
ggplot2::ggsave("MyRawData_f2.jpg", g, width=7, height=4, dpi=600)
data(onemap_example_out) # Loads a fake full-sib dataset installed with onemap

plot(onemap_example_out) # This will show you the graph for all markers
plot(onemap_example_out, all=FALSE) # This will show you the graph splitted for marker types
# You can store the graphic in an object, then save it.

g <- plot(onemap_example_out, all=FALSE)
ggplot2::ggsave("MyRawData_out.jpg", g, width=9, height=4, dpi=600)
## End(Not run)
plot.onemap_segreg_test
Plot p-values for chi-square tests of expected segregation
Description
Draw a graphic showing the p-values (re-scaled to -log10(p-values)) associated with the chi-square
tests for the expected segregation patterns for all markers in a dataset. It includes a vertical line
showing the threshold for declaring statistical significance if Bonferroni’s correction is considered,
as well as the percentage of markers that will be discarded if this criterion is used.
Usage
## S3 method for class 'onemap_segreg_test'
plot(x, order = TRUE, ...)
Arguments
x an object of class onemap_segreg_test (produced by onemap’s function test_segregation()),
i. e., after performing segregation tests
order a variable to define if p-values will be ordered in the plot
38 plot_by_segreg_type
Value
a ggplot graphic
Examples
data(onemap_example_bc) # load OneMap's fake dataset for a backcross population

BC.seg <- test_segregation(onemap_example_bc) # Applies chi-square tests
print(BC.seg) # Shows the results
plot(BC.seg) # Plot the graph, ordering the p-values
plot(BC.seg, order=FALSE) # Plot the graph showing the results keeping the order in the dataset
# g <- plot(BC.seg)
# ggplot2::ggsave("SegregationTests.jpg", g, width=7, height=5, dpi=600)
data(onemap_example_out) # load OneMap's fake dataset for an outcrossing population

Out.seg <- test_segregation(onemap_example_out) # Applies chi-square tests
print(Out.seg) # Shows the results
plot(Out.seg) # Plot the graph, ordering the p-values
plot(Out.seg, order=FALSE) # Plot the graph showing the results keeping the order in the dataset
g <- plot(Out.seg)
# ggplot2::ggsave("SegregationTests.jpg", g, width=7, height=5, dpi=600)
plot_by_segreg_type Draw a graphic showing the number of markers of each segregation

pattern.
Description
The function receives an object of class onemap. For outcrossing populations, it can show detailed
information (all 18 possible categories), or a simplified version.
Usage
plot_by_segreg_type(x, subcateg = TRUE)
Arguments
x an object of class onemap
subcateg a TRUE/FALSE option to indicate if results will be plotted showing all possible
categories (only for outcrossing populations)
Value
a ggplot graphic
print.onemap_segreg_test 39
Examples
data(onemap_example_out) #Outcrossing data
plot_by_segreg_type(onemap_example_out)
plot_by_segreg_type(onemap_example_out, subcateg=FALSE)
plot_by_segreg_type(onemap_example_bc)
plot_by_segreg_type(mapmaker_example_f2)

# data(onemap_example_out) #Outcrossing data
# g <- plot_by_segreg_type(onemap_example_out)
# ggplot2::ggsave("SegregationTypes.jpg", g, width=7, height=4, dpi=600)
print.onemap_segreg_test
Show the results of segregation tests
Description
It shows the results of Chisquare tests performed for all markers in a onemap object of cross type
outcross, backcross, F2 intercross or recombinant inbred lines.
Usage
## S3 method for class 'onemap_segreg_test'
print(x, ...)
Arguments
Value
a dataframe with marker name, H0 hypothesis, chi-square statistics, p-values, and
Examples
data(onemap_example_out) # Loads a fake outcross dataset installed with onemap
Chi <- test_segregation(onemap_example_out) # Performs the chi-square test for all markers
print(Chi) # Shows the results
40 rcd
rcd Rapid Chain Delineation
Description
Implements the marker ordering algorithm Rapid Chain Delineation (Doerge, 1996 ).
Usage
rcd(input.seq, LOD = 0, max.rf = 0.5, tol = 1e-04)
Arguments
LOD minimum LOD-Score threshold used when constructing the pairwise recombi-
nation fraction matrix.
max.rf maximum recombination fraction threshold used as the LOD value above.
Details
Rapid Chain Delineation (RCD) is an algorithm for marker ordering in linkage groups. It is not
an exhaustive search method and, therefore, is not computationally intensive. However, it does not
guarantee that the best order is always found. The only requirement is a matrix with recombina-
tion fractions between markers. Next is an excerpt from QTL Cartographer Version 1.17 Manual
describing the RCD algorithm (Basten et al., 2005 ):
The linkage group is initiated with the pair of markers having the smallest recombination fraction.
The remaining markers are placed in a “pool” awaiting placement on the map. The linkage group
is extended by adding markers from the pool of unlinked markers. Each terminal marker of the
linkage group is a candidate for extension of the chain: The unlinked marker that has the smallest
recombination fraction with either is added to the chain subject to the provision that the recombi-
nation fraction is statistically significant at a prespecified level. This process is repeated as long as
markers can be added to the chain.
After determining the order with RCD, the final map is constructed using the multipoint approach
(function map).
Value
to the input file.
rcd 41

Author(s)
References
Basten, C. J., Weir, B. S. and Zeng, Z.-B. (2005) QTL Cartographer Version 1.17: A Reference
Manual and Tutorial for QTL Mapping.
Doerge, R. W. (1996) Constructing genetic maps by rapid chain delineation. Journal of Quantitative
Trait Loci 2: 121-132.
See Also
make_seq, map
Examples
## Not run:
#outcross example
LG1.rcd <- rcd(LG1)
#F2 example
LG1.rcd <- rcd(LG1)
LG1.rcd
## End(Not run)
42 read_mapmaker
read_mapmaker Read data from a Mapmaker raw file
Description
Imports data from a Mapmaker raw file.
Usage
read_mapmaker(dir, file)
Arguments
dir directory where the input file is located.
file the name of the input file which contains the data to be read.
Details
For details about MAPMAKER files see Lincoln et al. (1993). The current version supports back-
cross, F2s and RIL populations. The file can contain phenotypic data, but it will not be used in the
analysis.
Value
geno a matrix with integers indicating the genotypes read for each marker in onemap
fashion. Each column contains data for a marker and each row represents an
individual.
geno.mmk a matrix with integers indicating the genotypes read for each marker in MAPMAKER/EXP
fashion, i.e., 1, 2, 3: AA, AB, BB, respectively; 3, 4: BB, not BB, respectively;
1, 5: AA, not AA, respectively. Each column contains data for a marker and
each row represents an individual.
segr.type a vector with the segregation type of each marker, as strings. Segregation
types were adapted from outcross segregation types, using the same notation.
For details see read_onemap.
manner as integers. Segregation types were adapted from outcross segregation
types. For details see read_onemap.
input the name of the input file.
row represents an individual. Currently ignored.
read_onemap 43
Author(s)
Adapted from Karl Broman (package qtl) by Marcelo Mollinari, <mmollina@usp.br>
References
See Also
mapmaker_example_bc and mapmaker_example_f2 directory in the package source.
Examples
## Not run:
map_data <-read_mapmaker(dir="work_directory",file="data_file.txt")
#Checking 'mapmaker_example_f2'
names(mapmaker_example_f2)
## End(Not run)
read_onemap Read data from all types of progenies supported by OneMap
Description
Imports data derived from outbred parents (full-sib family) or inbred parents (backcross, F2 in-
tercross and recombinant inbred lines obtained by self- or sib-mating). Creates an object of class
onemap.
Usage
read_onemap(dir, inputfile)
Arguments
dir directory where the input file is located.

inputfile the name of the input file which contains the data to be read.
44 read_onemap
Details
The file format is similar to that used by MAPMAKER/EXP (Lincoln et al., 1993). The first line
indicates the cross type and is structured as data type {cross}, where cross must be one of
"outcross", "f2 intercross", "f2 backcross", "ri self" or "ri sib". The second line con-
tains five integers: i) the number of individuals; ii) the number of markers; iii) an indicator variable
taking the value 1 if there is CHROM information, i.e., if markers are anchored on any reference
sequence, and 0 otherwise; iv) a similar 1/0 variable indicating whether there is POS information
for markers; and v) the number of phenotypic traits.
The next line contains sample IDs, separated by empty spaces or tabs. Addition of this sample ID
requirement makes it possible for separate input datasets to be merged.
Next comes the genotype data for all markers. Each new marker is initiated with a “*” (with-
out the quotes) followed by the marker name, without any space between them. Each marker
name is followed by the corresponding segregation type, which may be: "A.1", "A.2", "A.3",
"A.4", "B1.5", "B2.6", "B3.7", "C.8", "D1.9", "D1.10", "D1.11", "D1.12", "D1.13", "D2.14",
"D2.15", "D2.16", "D2.17" or "D2.18" (without quotes), for full-sibs [see marker_type and Wu
et al. (2002) for details]. Other cross types have special marker types: "A.H" for backcrosses;
"A.H.B" for F2 intercrosses; and "A.B" for recombinant inbred lines.
After the segregation type comes the genotype data for the corresponding marker. Depending on
the segregation type, genotypes may be denoted by ac, ad, bc, bd, a, ba, b, bc, ab and o, in several
possible combinations. To make things easier, we have followed exactly the notation used by Wu
et al. (2002). Allowed values for backcrosses are a and ab; for F2 crosses they are a, ab and b; for
RILs they may be a and b. Genotypes must be separated by a space. Missing values are denoted by
"-".
If there is physical information for markers, i.e., if they are anchored at specific positions in refer-
ence sequences (usually chromosomes), this is included immediately after the marker data. These
lines start with special keywords *CHROM and *POS and contain strings and integers, respectively,
indicating the reference sequence and position for each marker. These also need to be separated by
spaces.
Finally, if there is phenotypic data, it will be added just after the marker or CHROM/POS data. They
need to be separated by spaces as well, using the same symbol for missing information.
The example directory in the package distribution contains an example data file to be read with this
function. Further instructions can be found at the tutorial distributed along with this package.
Value
geno a matrix with integers indicating the genotypes read for each marker. Each col-
umn contains data for a marker and each row represents an individual.
segr.type a vector with the segregation type of each marker, as strings.
manner as integers, i.e. 1 corresponds to markers of type "A"; 2 corresponds
to markers of type "B1.5"; 3 corresponds to markers of type "B2.6"; 4 corre-
sponds to markers of type "B3.7"; 5 corresponds to markers of type "C.8"; 6
record 45
corresponds to markers of type "D1" and 7 corresponds to markers of type "D2".

Markers for F2 intercrosses are coded as 1; all other crosses are left as NA.
row represents an individual.
Author(s)
References
See Also
combine_onemap and the example directory in the package source.
Examples
## Not run:
outcr_data <- read_onemap(dir="work_directory", inputfile="data_file.txt")
## End(Not run)
record Recombination Counting and Ordering
Description
Implements the marker ordering algorithm Recombination Counting and Ordering (Van Os et al.,
2005 ).
Usage
record(input.seq, times = 10, LOD = 0, max.rf = 0.5, tol = 1e-04)

46 record
Arguments
times integer. Number of replicates of the RECORD procedure.
Details
Recombination Counting and Ordering (RECORD) is an algorithm for marker ordering in linkage
groups. It is not an exhaustive search method and, therefore, is not computationally intensive.
However, it does not guarantee that the best order is always found. The only requirement is a
matrix with recombination fractions between markers.
After determining the order with RECORD, the final map is constructed using the multipoint ap-
proach (function map).
Value
to the input file.
Author(s)
References
Van Os, H., Stam, P., Visser, R.G.F. and Van Eck, H.J. (2005) RECORD: a novel method for
ordering loci on a genetic linkage map. Theoretical and Applied Genetics 112: 30-40.
See Also
make_seq and map
rf_2pts 47
Examples
## Not run:
##outcross example
LG1.rec <- record(LG1)
##F2 example
LG1.rec <- record(LG1)
LG1.rec
## End(Not run)
rf_2pts Two-point analysis between genetic markers
Description
Performs the two-point (pairwise) analysis proposed by Wu et al. (2002) between all pairs of
markers.
Usage
rf_2pts(input.obj, LOD = 3, max.rf = 0.5, verbose = TRUE)
Arguments
LOD minimum LOD Score to declare linkage (defaults to 3).
max.rf maximum recombination fraction to declare linkage (defaults to 0.50).
verbose logical. If TRUE, current progress is shown; if FALSE, no output is produced.
Details
For n markers, there are
n(n − 1)
2
pairs of markers to be analyzed. Therefore, completion of the two-point analyses can take a long
time.
48 rf_graph_table
Value
An object of class rf_2pts, which is a list containing the following components:

analysis an array with the complete results of the two-point analysis for each pair of
markers.
Note
The thresholds used for LOD and max.rf will be used in subsequent analyses, but can be overriden.
Author(s)
Gabriel R A Margarido <gramarga@gmail.com> and Marcelo Mollinari <mmollina@usp.br>
References
Examples
twopts <- rf_2pts(onemap_example_out,LOD=3,max.rf=0.5) # perform two-point analyses

twopts
print(twopts,c("M1","M2")) # detailed results for markers 1 and 2
rf_graph_table Plots pairwise recombination fractions and LOD Scores in a heatmap
Description
Plots a matrix of pairwise recombination fraction or LOD Scores using a color scale. Any value of
the matrix can be easily accessed using an interactive plotly-html interface, helping users to check
for possible problems.
rf_graph_table 49
Usage
rf_graph_table(
input.seq,
graph.LOD = FALSE,
main = NULL,
inter = FALSE,
html.file = NULL,
mrk.axis = "numbers",
lab.xy = NULL,
n.colors = 4
)
Arguments
input.seq an object of class sequence with a predefined order.

graph.LOD logical. If TRUE, displays the LOD heatmap, otherwise, displays the recombina-
tion fraction heatmap.
main character. The title of the plot.
inter logical. If TRUE, an interactive HTML graphic is plotted. Otherwise, a default
graphic device is used.
html.file character naming the html file with iterative graphic.
mrk.axis character, "names" to display marker names in the axis, "numbers" to display
marker numbers and "none" to display axis free of labels.
lab.xy character vector with length 2, first component is the label of x axis and second
of the y axis.
n.colors integer. Number of colors in the pallete.
Details
The color scale varies from red (small distances or big LODs) to purple. When hover on a cell, a
dialog box is displayed with some information about corresponding markers for that cell (line (y)
× column (x)). They are: i) the name of the markers; ii) the number of the markers on the data
set; iii) the segregation types; iv) the recombination fraction between the markers and v) the LOD-
Score for each possible linkage phase calculated via two-point analysis. For neighbor markers,
the multipoint recombination fraction is printed; otherwise, the two-point recombination fraction
is printed. For markers of type D1 and D2, it is impossible to calculate recombination fraction via
two-point analysis and, therefore, the corresponding cell will be empty (white color). For cells on
the diagonal of the matrix, the name, the number and the type of the marker are printed, as well as
the percentage of missing data for that marker.
Author(s)
Rodrigo Amadeu, <rramadeu@gmail.com>

50 ripple_seq
Examples
## Not run:
##outcross example
LG1.rcd <- rcd(LG1)
rf_graph_table(LG1.rcd, inter=FALSE)
##Now, using interactive plotly

rf_graph_table(LG1.rcd, inter=TRUE, html.file= "LG1.rcd.html")
##F2 example
##"pre-allocate" an empty list of length groups$n.groups (3, in this case)

maps.list<-vector("list", groups$n.groups)
for(i in 1:groups$n.groups){
##create linkage group i
LG.cur <- make_seq(groups,i)
##ordering
map.cur<-order_seq(LG.cur, subset.search = "sample")
##assign the map of the i-th group to the maps.list
maps.list[[i]]<-make_seq(map.cur, "force")
}
##Plot LOD/recombination fraction matrices for each group
require(gridExtra)
plot1 <- rf_graph_table(maps.list[[1]], main="Group 1",inter=FALSE)
grid.arrange(plot1, plot2, plot3, nrow=3)
## End(Not run)
ripple_seq Compares and displays plausible alternative orders for a given linkage
group
Description
For a given sequence of ordered markers, computes the multipoint likelihood of alternative orders,
by shuffling subsets (windows) of markers within the sequence. For each position of the window,
all possible (ws)! orders are compared.
ripple_seq 51
Usage
ripple_seq(input.seq, ws = 4, ext.w = NULL, LOD = 3, tol = 0.1)
Arguments
ws an integer specifying the length of the window size (defaults to 4).
ext.w an integer specifying how many markers should be considered in the vicinity of
the permuted window. If ext.w=NULL all markers in the sequence are consid-
ered. In this veriosn, it is used only in backcross, F2 or RIL crosses.
LOD threshold for the LOD-Score, so that alternative orders with LOD less then or
equal to this threshold will be displayed.
Details
Large values for the window size make computations very slow, specially if there are many partially
informative markers.
Value
This function does not return any value; it just produces text output to suggest alternative orders.
Author(s)
Gabriel R A Margarido, <gramarga@gmail.com> and Marcelo Mollinari, <mmollina@usp.br>
References
349-363.
See Also
make_seq, compare, try_seq and order_seq.
52 select_segreg
Examples
## Not run:
#Outcross example
markers <- make_seq(twopt,c(27,16,20,4,19,21,23,9,24,29))
markers.map <- map(markers)
ripple_seq(markers.map)
#F2 example
LG3.ord
ripple_seq(ord.1, ws=5)
## End(Not run)
select_segreg Show markers with/without segregation distortion
Description
A function to shows which marker have segregation distortion if Bonferroni’s correction is applied
for the Chi-square tests of mendelian segregation.
Usage
select_segreg(x, distorted = FALSE, numbers = FALSE, threshold = NULL)
Arguments
distorted a TRUE/FALSE variable to show distorted or non-distorted markers
numbers a TRUE/FALSE variable to show the numbers or the names of the markers
threshold a number between 0 and 1 to specify the threshold to be considered in the test. If
NULL, it uses the threshold defined by bonferroni correction with alpha = 0.05
Value
a vector with marker names or numbers, according to the option for "distorted" and "numbers"
seriation 53
Examples
# Loads a fake backcross dataset installed with onemap
# Performs the chi-square test for all markers
Chi <- test_segregation(onemap_example_bc)
# To show non-distorted markers
select_segreg(Chi)
# To show markers with segregation distortion
select_segreg(Chi, distorted=TRUE)
# To show the numbers of the markers with segregation distortion
select_segreg(Chi, distorted=TRUE, numbers=TRUE)
seriation Seriation
Description
Implements the marker ordering algorithm Seriation (Buetow & Chakravarti, 1987 ).
Usage
seriation(input.seq, LOD = 0, max.rf = 0.5, tol = 1e-04)
Arguments
Details
Seriation is an algorithm for marker ordering in linkage groups. It is not an exhaustive search
method and, therefore, is not computationally intensive. However, it does not guarantee that the
best order is always found. The only requirement is a matrix with recombination fractions between
markers.
NOTE: When there are to many pairs of markers with the same value in the recombination fraction
matrix, it can result in ties during the ordination process and the Seriation algorithm may not work
properly. This is particularly relevant for outcrossing populations with mixture of markers of type
D1 and D2. When this occurs, the function shows the following error message: There are too many
ties in the ordination process -please,consider using another ordering algorithm.
After determining the order with Seriation, the final map is constructed using the multipoint ap-
proach (function map).
54 seriation
Value
to the input file.
Author(s)
References
Buetow, K. H. and Chakravarti, A. (1987) Multipoint gene mapping using seriation. I. General
methods. American Journal of Human Genetics 41: 180-188.
See Also
make_seq, map
Examples
## Not run:
##outcross example
LG3.ser <- seriation(LG3)
##F2 example
LG1.ser <- seriation(LG1)
LG1.ser
## End(Not run)
set_map_fun 55
set_map_fun Defines the default mapping function
Description
Defines the function that should be used to display the genetic map through the analysis.
Usage
set_map_fun(type = c("kosambi", "haldane"))
Arguments
type Indicates the function that should be used, which can be "kosambi" or "haldane"
Author(s)
References
Haldane, J. B. S. (1919) The combination of linkage values and the calculation of distance between
the loci of linked factors. Journal of Genetics 8: 299-309.
Kosambi, D. D. (1944) The estimation of map distance from recombination values. Annuaire of
Eugenetics 12: 172-175.
See Also
kosambi and haldane
suggest_lod Suggests a LOD Score for two point tests
Description
It suggests a LOD Score for declaring statistical significance for two-point tests for linkage between
all pairs of markers, considering that multiple tests are being performed.
Usage
suggest_lod(x)
Arguments
x an object of class onemap
56 test_segregation
Details
In a somehow naive approach, the function calculates the number of two-point tests that will be
performed for all markers in the data set, and then using this to calculate the global alpha required
to control type I error using Bonferroni’s correction.
From this global alpha, the corresponding quantile from the chi-square distribution is taken and
then converted to LOD Score.
This can be seen as just an initial approximation to help users to select a LOD Score for two point
tests.
Value
the suggested LOD to be used for testing linkage
Examples
suggest_lod(onemap_example_bc) # An value that should be used to start the analysis
test_segregation test_segregation
Description
Using OneMap internal function test_segregation_of_a_marker(), performs the Chi-square test to
check if all markers in a dataset are following the expected segregation pattern, i. e., 1:1:1:1 (A),
1:2:1 (B), 3:1 (C) and 1:1 (D) according to OneMap’s notation.
Usage
test_segregation(x)
Arguments
x an object of class onemap, with data and additional information.
Details
First, it identifies the correct segregation pattern and corresponding H0 hypothesis, and then tests it.
Value
an object of class onemap_segreg_test, which is a list with marker name, H0 hypothesis being
tested, the chi-square statistics, the associated p-values and the % of individuals genotyped. To see
the object, it is necessary to print it.
test_segregation_of_a_marker 57
Examples
data(onemap_example_out) # Loads a fake outcross dataset installed with onemap

Chi <- test_segregation(onemap_example_out) # Performs the chi-square test for all markers
print(Chi) # Shows the results
test_segregation_of_a_marker
test_segregation_of_a_marker
Description
Applies the chi-square test to check if markers are following the expected segregation pattern, i. e.,
1:1:1:1 (A), 1:2:1 (B), 3:1 (C) and 1:1 (D) according to OneMap’s notation. It does not use Yate’s
correction.
Usage
test_segregation_of_a_marker(x, marker)
Arguments
x an object of class onemap, with data and additional information.

marker the marker which will be tested for its segregation.
Details
First, the function selects the correct segregation pattern, then it defines the H0 hypothesis, and then
tests it, together with percentage of missing data.
Value
a list with the H0 hypothesis being tested, the chi-square statistics, the associated p-values, and the
% of individuals genotyped.
##’@examples data(onemap_example_bc) # Loads a fake backcross dataset installed with onemap
test_segregation_of_a_marker(onemap_example_bc,1)
data(onemap_example_out) # Loads a fake outcross dataset installed with onemap test_segregation_of_a_marker(onemap_ex
58 try_seq
try_seq Try to map a marker into every possible position between markers in
a given map
Description
For a given linkage map, tries do add an additional unpositioned marker. This function estimates
parameters for all possible maps including the new marker in all posible positions, while keeping
the original linkage map unaltered.
Usage
try_seq(input.seq, mrk, tol = 0.1, pos = NULL, verbose = FALSE)
Arguments

mrk the index of the marker to be tried, according to the input file.
pos defines in which position the new marker mrk should be placed for the diagnostic
graphic. If NULL (default), the marker is placed on the best position i.e. the one
which results LOD = 0.00
verbose if FALSE (default), simplified output is displayed. if TRUE, detailed output is
displayed.
Value
An object of class try, which is a list containing the following components:
ord a list containing results for every linkage map estimated. These results include
linkage phases, recombination frequencies and log-likelihoods.
LOD a vector with LOD-Scores for each position where the additional marker is
placed. This Score is based on the best combination of linkage phases for each
map.
try.ord a matrix with the orders of all linkage maps.
Author(s)

try_seq 59
References
rithms used to order markers on genetic maps. Heredity 103: 494-502
349-363.
See Also
make_seq and compare.
Examples
## Not run:
#outcrossing example
markers <- make_seq(twopt,c(2,3,12,14))
markers.comp <- compare(markers)
base.map <- make_seq(markers.comp,1)
extend.map <- try_seq(base.map,30)

extend.map
print(extend.map,5) # best position
print(extend.map,4) # second best position
#F2 example
twopt <- rf_2pts(mapmaker_example_f2)
LG3.ord
safe.map<-make_seq(LG3.ord,"safe")
extend.map <- try_seq(safe.map,64)
extend.map
(new.map<-make_seq(extend.map,14)) # best position
60 ug
## End(Not run)
ug Unidirectional Growth
Description
Implements the marker ordering algorithm Unidirectional Growth (Tan & Fu, 2006 ).
Usage
ug(input.seq, LOD = 0, max.rf = 0.5, tol = 1e-04)
Arguments
Details
Unidirectional Growth (UG) is an algorithm for marker ordering in linkage groups. It is not an
exhaustive search method and, therefore, is not computationally intensive. However, it does not
guarantee that the best order is always found. The only requirement is a matrix with recombination
fractions between markers.
After determining the order with UG, the final map is constructed using the multipoint approach
(function map).
Value
to the input file.
sponding positions. -1 means taht there are no defined linkage phases.
vcf2raw 61
Author(s)
References
Tan, Y. and Fu, Y. (2006) A novel method for estimating linkage maps. Genetics 173: 2383-2390.
See Also
make_seq, map
Examples
## Not run:
#outcross example
LG1.ug <- ug(LG1)
#F2 example
twopt <- rf_2pts(mapmaker_example_f2)
LG1.ug <- ug(LG1)
LG1.ug
## End(Not run)
vcf2raw Convert variants from a VCF file to OneMap file format
Description
Converts data from a standard VCF (Variant Call Format) file to the input format required by
OneMap, while trying to identify the appropriate marker segregation patterns.
62 vcf2raw
Usage
vcf2raw(
input = NULL,
output = NULL,
cross = c("outcross", "f2 intercross", "f2 backcross", "ri self", "ri sib"),
parent1 = NULL,
parent2 = NULL,
min_class = 1
)
Arguments
input path to the input VCF file.
output path to the output OneMap file.
cross type of cross. Must be one of: "outcross" for full-sibs; "f2 intercross" for
an F2 intercross progeny; "f2 backcross"; "ri self" for recombinant inbred
lines by self-mating; or "ri sib" for recombinant inbred lines by sib-mating.
parent1 string or vector of strings specifying sample ID(s) of the first parent.
parent2 string or vector of strings specifying sample ID(s) of the second parent.
min_class a real number between 0.0 and 1.0. For each parent and each variant site, defines
the proportion of parent samples that must be of the same genotype for it to be
assigned to the corresponding parent.
Details
The input VCF file must be sorted, compressed and tabix indexed. Please check functions bgzip
and indexTabix of package Rsamtools for details.
Each variant in the VCF file is processed independently. Only biallelic SNPs and indels for diploid
variant sites are considered.
Genotype information on the parents is required for all cross types. For full-sib progenies, both
outbred parents must be genotyped. For backcrosses, F2 intercrosses and recombinant inbred lines,
the original inbred lines must be genotyped. Particularly for backcross progenies, the recurrent line
must be provided as the first parent in the function arguments.
First, samples corresponding to both parents of the progeny are parsed and their genotypes identi-
fied, given that their replicates are concordant above a threshold given by min_class. This allows
replicates of the parents to be used, which is common in sequencing plates. In detail, each parent
will be called an heterozygote only if min_class ∗ number of replicates samples or more are het-
erozygous. The same is valid for homozygous calls. Whenever there are different genotypes among
replicates, heterozygosity is checked first. The default value (1.0) requires that all replicates be of
the same genotype. If each parent is represented by a single sample, this parameter has no effect.
Next, marker type is determined based on parental genotypes. Finally, progeny genotypes are iden-
tified and output is produced. Variants for which parent genotypes cannot be determined are dis-
carded.
Reference sequence ID and position for each variant site are stored as special fields denoted CHROM
and POS.
vcf_example_bc 63
Author(s)
See Also
read_onemap for a description of the OneMap file format.
Examples
## Not run:
vcf2raw(input="your_VCF_file.vcf.gz",
output="your_OneMap_file.raw",
cross="your_cross_type",
parent1=c("PAR1_sample1", "PAR1_sample2"),
parent2=c("PAR2_sample1", "PAR2_sample2", "PAR2_sample3"),
min_class=0.5) # for parent1, a single heterozygote replicate results
# in a heterozygote genotype call; for parent2, at
# least two samples have to be concordant
## End(Not run)
vcf_example_bc Data generated from VCF file with biallelic markers from a f2 back-
cross population
Description
Simulated biallelic data set for an backcross population
Usage
data("vcf_example_bc")
Format
Details
A total of 142 backcross individuals were genotyped with 25 markers. The data was generated from
a VCF file. It contains chromossome and position informations for each marker. It is included to be
used as a example in order to understand how to convert VCF file to OneMap input data with the
functions vcf2raw and onemap_read_vcfR.
Author(s)
Cristiane Hayumi Taniguti, <chaytaniguti@gmail.com>
64 vcf_example_f2
See Also
Examples
data(vcf_example_bc)
plot(vcf_example_bc)
vcf_example_f2 Data generated from VCF file with biallelic markers from a f2 inter-
cross population
Description
Simulated biallelic data set for an f2 population
Usage
data(vcf_example_f2)
Format
Details
A total of 192 F2 individuals were genotyped with 25 markers. The data was generated from a VCF
file. It contains chromossome and position informations for each marker. It is included to be used
as a reference in order to understand how to convert VCF file to OneMap input data. Also, it is used
for the analysis in the tutorial that comes with OneMap.
Author(s)
See Also
Examples
data(vcf_example_f2)
# plot markers informations

plot(vcf_example_f2)
vcf_example_out 65
vcf_example_out Data generated from VCF file with biallelic markers from a full-sib
family derived from two outbred parents
Description
Simulated biallelic data set for an outcross, i.e., an F1 population obtained by crossing two non-
homozygous parents.
Usage
data(vcf_example_out)
Format
Details
A total of 92 F1 individuals were genotyped with 27 markers. The data was generated from a VCF
file. It contains chromossome and position informations for each marker. It is included to be used
as a reference in order to understand how to convert VCF file to OneMap input data. Also, it is used
for the analysis in the tutorial that comes with OneMap.
Author(s)
See Also
Examples
data(vcf_example_out)
# plot markers informations

plot(vcf_example_out)
66 vcf_example_riself
vcf_example_riself Data generated from VCF file with biallelic markers from a RIL pop-
ulation produced by selfing
Description
Simulated biallelic data set for an ri self population.
Usage
data("vcf_example_riself")
Format
of 2 .. ..$ : chr [1:92] "ID1" "ID3" "ID4" "ID5" ... .. ..$ : chr [1:25] "SNP16" "SNP12" "SNP17"
"SNP10" ... $ n.ind : int 92 $ n.mar : int 25 $ segr.type : chr [1:25] "A.B" "A.B" "A.B" "A.B"
... $ segr.type.num: logi [1:25] NA NA NA NA NA NA ... $ n.phe : int 0 $ pheno : NULL $
CHROM : chr [1:25] "1" "1" "1" "1" ... $ POS : int [1:25] 1791 6606 9001 11326 11702 15533
17151 18637 19146 19220 ... $ input : chr "vcf_example_riself.raw" - attr(*, "class")= chr [1:2]
"onemap" "riself"
Details
A total of 92 rils individuals were genotyped with 25 markers. The data was generated from a VCF
file. It contains chromossome and position informations for each marker. It is included to be used as
a example in order to understand how to convert VCF file to OneMap input data with the functions
vcf2raw and onemap_read_vcfR.
Author(s)
See Also
Examples
data(vcf_example_riself)
plot(vcf_example_riself)
write_map 67
write_map Write a genetic map to a file
Description
Write a genetic map to a file, base on a given map, or a list of maps. The output file can be used as
an input to perform QTL mapping using the package R/qtl. It is also possible to create an output to
be used with QTLCartographer program.
Usage
write_map(map.list, file.out)
Arguments
map.list a map, i.e. an object of class sequence with a predefined order, linkage phases,
recombination fraction and likelihood or a list of maps.
file.out output map file.
Details
This function is avaliable only for backcross, F2 and RILs.
Author(s)
References
Wang S., Basten, C. J. and Zeng Z.-B. (2010) Windows QTL Cartographer 2.5. Department of
Statistics, North Carolina State University, Raleigh, NC.
Examples
## Not run:
twopt<-rf_2pts(mapmaker_example_f2)
##"pre-allocate" an empty list of length lg$n.groups (3, in this case)

maps.list<-vector("list", lg$n.groups)
for(i in 1:lg$n.groups){
##create linkage group i
LG.cur <- make_seq(lg,i)
68 write_onemap_raw
##ordering
map.cur<-order_seq(LG.cur, subset.search = "sample")
##assign the map of the i-th group to the maps.list
maps.list[[i]]<-make_seq(map.cur, "force")
}
##write maps.list to "mapmaker_example_f2.map" file

write_map(map.list, "mapmaker_example_f2.map")
##Using R/qtl
##you must install the package 'qtl'
##install.packages("qtl")
require(qtl)
file<-paste(system.file("example",package="onemap"),"mapmaker_example_f2.raw", sep="/")
dat1 <- read.cross("mm", file=file, mapfile="mapmaker_example_f2.map")
newmap <- est.map(dat1, tol=1e-6, map.function="kosambi")
(logliks <- sapply(newmap, attr, "loglik"))

plot.map(dat1, newmap)
##Using R/qtl to generate QTL Cartographer input files (.map and .cro)
write.cross(dat1, format="qtlcart", filestem="mapmaker_example_f2")
## End(Not run)
write_onemap_raw Convert onemap object to onemap raw file
Description
Converts onemap R object to onemap input file. The input file brings information about the mapping
population: First line: cross type, it can be "outcrossing", "f2 intercross", "f2 backcross", "ri self"
or "ri sib". Second line: number of individuals, number of markers, presence (1) or absence (0)
of chromossome and position of the markers, and number of phenotypes mesured. Third line:
Individuals/sample names; Followed lines: marker name, marker type and genotypes. One line for
each marker. Final lines: chromossome, position and phenotypes informations. See more about
input file format at vignettes.
Usage
write_onemap_raw(
onemap.obj = NULL,
file.name = "out.raw",
cross = c("outcross", "f2 backcross", "f2 intercross", "ri self", "ri sib")
)
write_onemap_raw 69
Arguments
onemap.obj object of class ‘onemap‘
file.name a character for the onemap raw file name. Default is "out.raw"
cross a character describing the cross type. It can be "outcrossing", "f2 intercross",
"f2 backcross", "ri self" or "ri sib"
Author(s)
See Also
read_onemap for a description of the output object of class onemap.
Examples
## Not run:
write_onemap_raw(onemap_example_out, file.name = "onemap_example_out.raw", cross="outcross")
## End(Not run)
Index
∗Topic IO map, 20
combine_onemap, 5 marker_type, 25
read_mapmaker, 42 order_seq, 33
read_onemap, 43 rcd, 40
vcf2raw, 61 record, 45
∗Topic arith rf_2pts, 47
map_func, 24 rf_graph_table, 48
set_map_fun, 55 ripple_seq, 50
∗Topic bins seriation, 53
create_data_bins, 9 try_seq, 58
find_bins, 14 ug, 60
∗Topic datasets
mapmaker_example_bc, 22 add_marker, 3, 13
mapmaker_example_f2, 23
Bonferroni_alpha, 4
onemap_example_bc, 28
onemap_example_f2, 29 combine_onemap, 5, 45
onemap_example_out, 30 compare, 6, 20, 33, 35, 51, 59
onemap_example_riself, 31 create_data_bins, 9, 14
vcf_example_bc, 63 create_dataframe_for_plot_outcross, 8
vcf_example_f2, 64
vcf_example_out, 65 draw_map, 10
vcf_example_riself, 66 draw_map2, 11
∗Topic dimension drop_marker, 4, 13
create_data_bins, 9
find_bins, 14 find_bins, 9, 14
∗Topic manip
marker_type, 25 group, 15, 18
∗Topic misc group_seq, 16
group, 15
haldane, 55
∗Topic reduction
haldane (map_func), 24
create_data_bins, 9
find_bins, 14 kosambi, 55
∗Topic rqtl kosambi (map_func), 24
draw_map, 10
draw_map2, 11 make_seq, 7, 16, 18, 18, 21, 26, 35, 41, 46, 51,
write_map, 67 54, 59, 61
∗Topic utilities map, 20, 20, 40, 41, 46, 53, 54, 60, 61
compare, 6 map_func, 24
make_seq, 18 mapmaker_example_bc, 22
70
INDEX 71
mapmaker_example_f2, 23
marker_type, 7, 25, 44
mds_onemap, 26
onemap_example_bc, 28
onemap_example_f2, 29
onemap_example_out, 30
onemap_example_riself, 31
onemap_read_vcfR, 32
order_seq, 20, 33, 51
plot.onemap, 36
plot.onemap_segreg_test, 37
plot_by_segreg_type, 38
print.onemap_segreg_test, 39
rcd, 40
read_mapmaker, 6, 22, 29, 42
read_onemap, 6, 22, 29–31, 42, 43, 64–66
record, 45
rf_2pts, 16, 47
rf_graph_table, 48
ripple_seq, 50
select_segreg, 52
seriation, 53
set_map_fun, 55
suggest_lod, 55
test_segregation, 56
test_segregation_of_a_marker, 57
try_seq, 20, 35, 51, 58
ug, 60
vcf2raw, 61
vcf_example_bc, 63
vcf_example_f2, 64
vcf_example_out, 65
vcf_example_riself, 66
write_map, 67
write_onemap_raw, 68

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add_marker Creates a new sequence by adding markers.

@author Marcelo Mollinari, <mmollina@usp.br>

Bonferroni_alpha Calculates individual significance level to be used to achieve a global

Bonferroni_alpha(x, global.alpha = 0.05)

x an object of class onemap_segreg_test

the alpha value for each test (numeric)

combine_onemap Combine OneMap datasets

Gabriel R A Margarido, <gramarga@gmail.com>

read_onemap and read_mapmaker.

compare(input.seq, n.best = 50, tol = 0.001, verbose = FALSE)

input.seq an object of class sequence.

create_data_bins New dataset based on bins

Creates a new dataset based on onemap_bin object

input.obj an object of class onemap.

an object of class onemap.

Marcelo Mollinari, <mmollina@usp.br>

draw_map Draw a genetic map

draw_map2 Draw a linkage map

pos logical. If TRUE (default), shows position(s) of tagged marker(s).

drop_marker Creates a new sequence by dropping markers.

@author Marcelo Mollinari, <mmollina@usp.br>

find_bins Allocate markers into bins

find_bins(input.obj, exact = TRUE, ch = NULL)

input.obj an object of class onemap.

An object of class onemap_bin, which is a list containing the following components:

Marcelo Mollinari, <mmollina@usp.br>

group Assign markers to linkage groups

Gabriel R A Margarido, <gramarga@gmail.com> and Marcelo Mollinari, <mmollina@usp.br>

rf_2pts and make_seq

all.data <- make_seq(twopts,"all")

group_seq Assign markers to preexisting linkage groups

out_CHROM <- group_seq(twopts, seqs="CHROM", repeated=FALSE)

seq1 <- make_seq(twopts, c(1,2,3,4,5,25,26))

out_seqs <- group_seq(twopts, seqs=list(seq1,seq2,seq3))

make_seq Create a sequence of markers

all_mark <- make_seq(twopt,"all")

markers <- make_seq(twopt,c(2,3,12,14))

map Construct the linkage map for a sequence of markers

markers <- make_seq(twopt,c(30,12,3,14,2)) # correct phases

markers <- make_seq(twopt,c(30,12,3,14,2),phase=c(4,1,4,3)) # incorrect phases

mapmaker_example_bc Simulated data from a backcross population

Simulated data set from a backcross population.

Marcelo Mollinari, <mmollina@usp.br>

read_onemap and read_mapmaker.

# perform two-point analyses

mapmaker_example_f2 Simulated data from a F2 population

Simulated data set from a F2 population.

# perform two-point analyses

map_func Mapping functions Haldane and Kosambi

Functions to convert recombination fractions to distance in cM (centiMorgans).

Haldane mapping function is defined as

Both functions return a number with a distance measured in cM.

Gabriel R A Margarido, <gramarga@gmail.com>

# greater difference as recombination fraction increases

marker_type Informs the segregation patterns of markers

Type Cross Segregation

mds_onemap OneMap interface with MDSMap package with possibilitie of multi-

onemap_example_bc Simulated data from a backcross population

# perform two-point analyses

onemap_example_f2 Simulated data from a F2 population