TFsEnrichInRegions {enrichTF}R Documentation

Test each TF is enriched in regions or not

Description

Test each TF is enriched in regions or not

Usage

enrichTFsEnrichInRegions(enrichStep, inputRegionBed = NULL,
  inputForegroundGeneBed = NULL, inputBackgroundGeneBed = NULL,
  inputRegionMotifBed = NULL, outputTFsEnrichTxt = NULL,
  inputMotifWeights = NULL, inputTFgeneRelMtx = NULL,
  inputMotifTFTable = NULL, ...)

## S4 method for signature 'Step'
enrichTFsEnrichInRegions(enrichStep,
  inputRegionBed = NULL, inputForegroundGeneBed = NULL,
  inputBackgroundGeneBed = NULL, inputRegionMotifBed = NULL,
  outputTFsEnrichTxt = NULL, inputMotifWeights = NULL,
  inputTFgeneRelMtx = NULL, inputMotifTFTable = NULL, ...)

tfsEnrichInRegions(inputRegionBed, inputForegroundGeneBed,
  inputBackgroundGeneBed, inputRegionMotifBed, outputTFsEnrichTxt = NULL,
  inputMotifWeights = NULL, inputTFgeneRelMtx = NULL,
  inputMotifTFTable = NULL, ...)

Arguments

enrichStep

Step-class object scalar. It has to be the return value of upstream process from regionConnectTargetGene, regionConnectTargetGene, findMotifsInRegions or enrichFindMotifsInRegions, If it is used in a pipeline or %>% is applied on this function, any steps in this package is acceptable.

inputRegionBed

Character scalar. Directory of Regions BED file including foreground and background

inputForegroundGeneBed

Character scalar. Directory of BED file including foreground regions connected to related genes. The forth column is region ID

inputBackgroundGeneBed

Character scalar. Directory BED file including foreground regions connected to related genes. The forth column is region ID

inputRegionMotifBed

Character scalar. Directory BED file including foreground regions matched motifs. The forth column is region ID. The fifth column is motif calling score. The sixth column is motif name.

outputTFsEnrichTxt

Character scalar. Directory of Text result file with five columns. The first columns is transcription factor ,The second column is xxxx

inputMotifWeights

Character scalar. Directory of Text file contain motif weight. The first column is motif name. The second column is the weight. Default: NULL (if setGenome is called.)

inputTFgeneRelMtx

Character scalar. Directory of Text file contain a Transcription Factior(TF) and Gene relation weight matrix. Default: NULL (if setGenome is called.)

inputMotifTFTable

Character scalar. Directory of Text file contain Transcription Factior(TF) (the first column) and motif name(the second column). Default: NULL (if setGenome is called.)

...

Additional arguments, currently unused.

Details

Connect foreground and background regions to targetGene. If you only use this function without previous steps and you do not familiar with the data format of the input, you can run the example to see the example input from previous steps.

Value

An invisible EnrichStep-class object (Step-class based) scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

genBackground findMotifsInRegions tfsEnrichInRegions

Examples


library(magrittr)
setGenome("testgenome") #Use "hg19","hg38",etc. for your application
foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed")
gen <- genBackground(inputForegroundBed = foregroundBedPath)
conTG <- enrichRegionConnectTargetGene(gen)
findMotif <- enrichFindMotifsInRegions(gen,motifRc="integrate")
result <- enrichTFsEnrichInRegions(gen)

genBackground(inputForegroundBed = foregroundBedPath) %>%
    enrichRegionConnectTargetGene %>%
    enrichFindMotifsInRegions(motifRc="integrate") %>%
    enrichTFsEnrichInRegions


[Package enrichTF version 1.0.0 Index]