RegionConnectTargetGene: Connect regions with their target genes

In enrichTF: Transcription Factors Enrichment Analysis

Description

Connect foreground and background regions to their target genes, which is predicted from PECA model.

Usage

enrichRegionConnectTargetGene(
  prevStep,
  inputForegroundBed = NULL,
  inputBackgroundBed = NULL,
  outputForegroundBed = NULL,
  outputBackgroundBed = NULL,
  regularGeneCorrBed = NULL,
  enhancerRegularGeneCorrBed = NULL,
  ouputForgroundGeneTxt = NULL,
  ...
)

## S4 method for signature 'Step'
enrichRegionConnectTargetGene(
  prevStep,
  inputForegroundBed = NULL,
  inputBackgroundBed = NULL,
  outputForegroundBed = NULL,
  outputBackgroundBed = NULL,
  regularGeneCorrBed = NULL,
  enhancerRegularGeneCorrBed = NULL,
  ouputForgroundGeneTxt = NULL,
  ...
)

regionConnectTargetGene(
  inputForegroundBed,
  inputBackgroundBed,
  outputForegroundBed = NULL,
  outputBackgroundBed = NULL,
  regularGeneCorrBed = NULL,
  enhancerRegularGeneCorrBed = NULL,
  ouputForgroundGeneTxt = 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.
inputForegroundBed	Character scalar. The BED file directory of foreground regions.
inputBackgroundBed	Character scalar. The BED file directory of background regions.
outputForegroundBed	Character scalar. The BED file directory of target genes connecting with foreground regions, which are derived from PECA model. Default: NULL (generated base on inputForegroundBed)
outputBackgroundBed	Character scalar. The BED file directory of target genes connecting with background regions, which are derived from PECA model. Default: NULL (generated base on inputBackgroundBed)
regularGeneCorrBed	Character scalar. The BED file directory of target genes which are predicted from PECA. Default: NULL (e.g. after library (enrichTF), you can call function setGenome("hg19"))
enhancerRegularGeneCorrBed	Character scalar. The BED file directory of enhancer-targets predicted from PECA. Default: NULL (e.g. after library (enrichTF), you can call function setGenome("hg19"))
ouputForgroundGeneTxt	Character scalar. The TXT file directory of target genes list connecting with foreground regions, which are derived from PECA model. Default: NULL (generated base on inputForegroundBed)
...	Additional arguments, currently unused.

Details

Connect foreground and background regions to target genes, which are predicted from PECA.

Value

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

Author(s)

Zheng Wei

See Also

genBackground findMotifsInRegions tfsEnrichInRegions

Examples

setGenome("testgenome") #Use "hg19","hg38",etc. for your application
foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed")
gen <- genBackground(inputForegroundBed = foregroundBedPath)
conTG <- enrichRegionConnectTargetGene(gen)

enrichTF documentation built on Nov. 8, 2020, 6:15 p.m.