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, 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)

[Package enrichTF version 1.2.3 Index]