GenBackground: Generate background regions and reset the size of foreground...

In wzthu/enrichTF: Transcription Factors Enrichment Analysis

Description

Use uniform distribution to generate background sequence regions from genome. The size of foreground regions will be unified into the length specified in argument.

Usage

enrichGenBackground(
  prevStep,
  inputForegroundBed = NULL,
  inputBackgroundBed = NULL,
  genome = NULL,
  outputForegroundBed = NULL,
  outputBackgroundBed = NULL,
  outputRegionBed = NULL,
  regionLen = 1000,
  sampleNumb = 10000,
  ...
)

## S4 method for signature 'Step'
enrichGenBackground(
  prevStep,
  inputForegroundBed = NULL,
  inputBackgroundBed = NULL,
  genome = NULL,
  outputForegroundBed = NULL,
  outputBackgroundBed = NULL,
  outputRegionBed = NULL,
  regionLen = 1000,
  sampleNumb = NULL,
  ...
)

genBackground(
  inputForegroundBed,
  inputBackgroundBed = NULL,
  genome = NULL,
  outputForegroundBed = NULL,
  outputBackgroundBed = NULL,
  outputRegionBed = NULL,
  regionLen = 1000,
  sampleNumb = NULL,
  ...
)

Arguments

prevStep	Step-class object scalar. It needs to be the return value of upstream process from other packages, such as esATAC.
inputForegroundBed	Character scalar. The directory of foreground BED file.
inputBackgroundBed	Character scalar. The directory of backgroud BED file. Default: NULL to generate random region from genome.
genome	Character scalar. Bioconductor supported genome such as "hg19", "mm10", etc. Default: NULL (e.g. after library (enrichTF), you can call function setGenome("hg19"))
outputForegroundBed	Character scalar. The BED file directory of reshaped foreground regions. Default: NULL (generated base on inputForegroundBed)
outputBackgroundBed	Character scalar. The BED file directory of reshaped background regions. Default: NULL (generated base on inputForegroundBed)
outputRegionBed	Character scalar. Foreground and background merged BED files. Default: NULL (generated base on inputForegroundBed)
regionLen	Character scalar. It sets the length of forground sequence regions. Default: 1000
sampleNumb	numeric scalar. It sets the number of background regions that will be sampled. Default: 10000
...	Additional arguments, currently unused.

Details

Use uniform distribution to generate background sequence regions from genome. The size of foreground regions will be unified into the length specified in argument.

Value

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

Author(s)

Zheng Wei

See Also

regionConnectTargetGene findMotifsInRegions tfsEnrichInRegions

Examples

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

wzthu/enrichTF documentation built on March 30, 2020, 1:51 p.m.