TFsEnrichInRegions: Test each TF is enriched in regions or not

In wzthu/enrichTF: Transcription Factors Enrichment Analysis

Description

Test each TF is enriched in regions or not

Usage

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

## S4 method for signature 'Step'
enrichTFsEnrichInRegions(
  prevStep,
  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

prevStep	Step-class object scalar. This parameter is available when the upstream step function (printMap() to see the previous functions) have been sucessfully called. Accepted value can be the object return by any step function or be feed by %>% from last step function.
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

wzthu/enrichTF documentation built on March 30, 2020, 1:51 p.m.