RegionConnectTargetGene {enrichTF}R Documentation

Connect regions with their target genes

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, ...)

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

regionConnectTargetGene(inputForegroundBed, inputBackgroundBed,
  outputForegroundBed = NULL, outputBackgroundBed = NULL,
  regularGeneCorrBed = NULL, enhancerRegularGeneCorrBed = NULL, ...)

Arguments

prevStep

Step-class object scalar. It needs to be the return value of upstream process from genBackground or enrichGenBackground when it is not used in a pipeline. If it is used in a pipeline or %>% is applied on this function, any steps in this package is acceptable.

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"))

...

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)

[Package enrichTF version 1.0.0 Index]