get.tab {ELMER} | R Documentation |
summarize MR TF as a binary table with 1 if TF was found in the analysis, 0 if not
get.tab(dir, classification, top = TRUE)
dir |
Directory with ELMER results |
classification |
Which columns to retrieve family or subfamily |
top |
Consider only top 1 within each (sub)family |
## Not run: dir.create("out") dir.create("out2") data <- tryCatch( ELMER:::getdata("elmer.data.example"), error = function(e) { message(e) data(elmer.data.example, envir = environment()) }) enriched.motif <- list("P53_HUMAN.H11MO.1.A"= c("cg00329272", "cg10097755", "cg08928189", "cg17153775", "cg21156590", "cg19749688", "cg12590404", "cg24517858", "cg00329272", "cg09010107", "cg15386853", "cg10097755", "cg09247779", "cg09181054")) TF <- get.TFs(data, enriched.motif, group.col = "definition", group1 = "Primary solid Tumor", group2 = "Solid Tissue Normal", TFs = data.frame( external_gene_name=c("TP53","TP63","TP73"), ensembl_gene_id= c("ENSG00000141510", "ENSG00000073282", "ENSG00000078900"), stringsAsFactors = FALSE), dir.out = "out", label="hypo") TF <- get.TFs(data, enriched.motif, group.col = "definition", group1 = "Primary solid Tumor", group2 = "Solid Tissue Normal", TFs = data.frame( external_gene_name=c("TP53","TP63","TP73"), ensembl_gene_id= c("ENSG00000141510", "ENSG00000073282", "ENSG00000078900"), stringsAsFactors = FALSE), dir.out = "out2", label="hypo") ta.family <- get.tab(dir = c("out","out2"),classification = "family") ta.subfamily <- get.tab(dir = c("out","out2"),classification = "subfamily") unlink("out") unlink("out2") ## End(Not run)