非負値テンソル分解を用いた細胞間コミュニケーション検出
- 8. X
- 9. X X1 X2 X3 ^ ^ ^
- 10. X u1'◦v1' u2'◦v2' u3'◦v3' X1 X2 X3 ^ ^ ^
- 11. X u1'◦v1' u2'◦v2' u3'◦v3' u1◦v1 u2◦v2 u3◦v3 X1 X2 X3 ^ ^ ^ λ1 λ2 λ3
- 12. X u1'◦v1' u2'◦v2' u3'◦v3' u1◦v1 u2◦v2 u3◦v3 UΛVT X1 X2 X3 ^ ^ ^ λ1 λ2 λ3
- 14. χ S S
- 18. x y z
- 20. a(3)3: a(1)2: a(2)1: (2, 1, 3)
- 22. library(scTensor) library(SingleCellExperiment) library(LRBase.Hsa.eg.db) data(“GermMale”) # Data matrix (486genes × 852cells, 7class, 3.5MB) data(“tsneGermMale”) # The result of Rtsne (21kb) data(“labelGermMale”) # Celltype label (15kb) sce <- SingleCellExperiment(assays = list(counts = GermMale)) reducedDims(sce) <- SimpleList(TSNE = tsneGermMale$Y) cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale)) rks <- cellCellRanks(sce) cellCellDecomp(sce, ranks=rks) cellCellReport(sce, reducedDimNames="TSNE", out.dir=tmp, title="Cell-cell interaction within Germline, Male, GSE86146", author="Koki Tsuyuzaki", thr=80)