get.tab: summarize MR TF as a binary table with 1 if TF was found in...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

summarize MR TF as a binary table with 1 if TF was found in the analysis, 0 if not

Usage

get.tab(dir, classification, top = TRUE)

Arguments

dir	Directory with ELMER results
classification	Which columns to retrieve family or subfamily
top	Consider only top 1 within each (sub)family

Examples

## 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)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.