This program contains code for running LOCC analysis on TCGA LIHC data. You will need to download the TCGA Liver hepatocellular carcinoma dataset. I have also included E2F1 expression data from LIRI-JP in the downloads.

Install R and R studio. Input Code into a new script.

Install packages, which are located at the top of the code.

Download the TCGA dataset from [https://www.cbioportal.org/datasets]

Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas)

Move folder (lihc_tcga_pan_can_atlas_2018) to suitable directory and set directory to that location.

#Set Directory

setwd("C:/Users/soldi/Documents/R/CTRP2")

Copy and replace that old directory location to the new directory location for all of the code.

Add the LIRIJP_E2F1_Ranked.csv to the folder (lihc_tcga_pan_can_atlas_2018).

The Loccfunc function will calculate LOCC and AUC and save pictures of graphs related to LOCC and AUC for a gene of interest in the TCGA dataset. The gene of interest will be located at j where j is the row number of the gene in the TCGA expression dataset. You can query a gene of interest by replacing "E2F1" in grep("E2F1"...) with your gene of interest.

j <- grep("E2F1", PtExpressionZ$Hugo_Symbol)

The LOCC analysis can will take a long time to run if it attempts to analyze LOCC scores for every single gene. I would recommend not running this particular loop until all the other code can be run. If you # out these lines, you can run the rest of the code to make sure it works.

#Loop over all genes, will take a long time

for (j in 1:20531){ Loccfunc(j) }

The other code after the loop include LOCC and AUC analysis of other gene sets (RISK/8-gene RISK) and samples of genes.