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

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

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

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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

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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)

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