get.tab {ELMER} | R Documentation

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

### 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)

[Package ELMER version 2.12.0 Index]