| 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)