RegionConnectTargetGene: Connect regions with their target genes

Description Usage Arguments Details Value Author(s) See Also Examples

Description

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

Usage

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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

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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.