TissueOpennessConserve: Tissue's open conservation of the given region

In enrichTF: Transcription Factors Enrichment Analysis

Description

User provide region through a BED file. This function will provide tissue's open conservation analysis for these region.

Usage

enrichTissueOpennessConserve(
  prevStep,
  bedInput = NULL,
  openConserveBedInput = NULL,
  bedOutput = NULL,
  distrPdfOutput = NULL,
  ...
)

## S4 method for signature 'Step'
enrichTissueOpennessConserve(
  prevStep,
  bedInput = NULL,
  openConserveBedInput = NULL,
  bedOutput = NULL,
  distrPdfOutput = NULL,
  ...
)

tissueOpennessConserve(
  bedInput,
  openConserveBedInput = NULL,
  bedOutput = NULL,
  distrPdfOutput = 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.
bedInput	Character scalar. The directory of region BED file for analysis.
openConserveBedInput	Character scalar. The open level BED file for analysis. The first three columns are chromosome, start and end, The remaining columns are region name and conservation score.
bedOutput	Character scalar. The BED output file directory of merged BED files. Default: NULL (generated base on bedInput)
distrPdfOutput	Character scalar. The open conservation distribution figure for each tissue will be provided in PDF file.
...	Additional arguments, currently unused.

Details

We collected 201 DNase-seq or ATAC-seq sample from ENCODE and calculate their open level value. They can be download and install automatically. So users do not need to configure themselves.

Value

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

Author(s)

Zheng Wei

See Also

unzipAndMergeBed

Examples

foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed")
tissueOpennessConserve(bedInput = foregroundBedPath)

enrichTF documentation built on Nov. 8, 2020, 6:15 p.m.