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]