PECA_TF_enrich {enrichTF}R Documentation

TF enrichment with PECA model

Description

This is a pipeline for TF enrichment with PECA model.

Usage

PECA_TF_enrich(inputForegroundBed, genome, threads = 2, ...)

Arguments

inputForegroundBed

Character scalar. Foreground BED file directory.

genome

Character scalar. Bioconductor supported genome like "hg19", "mm10", etc.

threads

Numeric scalar. The max number of threads that can be used by each step of the pipeline

...

Additional arguments to set arguments for each Steps. See below for details.

Details

This is a function for the pipeline. There are four steps in this pipeline: GenBackground, RegionConnectTarget, FindMotifsInRegions and TFsEnrichInRegions. Parameter setting is available for all these functions. For example, if you want to change the number of background regions (sampleNumb) into 1000, you can add the argument GenBackground.sampleNumb = 1000 into the function like this: PECA_TF_enrich(inputForegroundBed = "your_file.bed", genome="hg19",GenBackground.sampleNumb = 1000). The number of arguments is not limited so you can add other arguments with the format (StepName.argumentName) in the same way.

Value

An invisible list contains all four steps EnrichTF objects

Author(s)

Zheng Wei

References

Zhana Duren, et al., Modeling gene regulation from paired expression and chromatin accessibility data. Proc Natl Acad Sci U S A. 2017 1;111(44):15675-80

Examples


foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed")
# This is the whole pipeline example.
PECA_TF_enrich(inputForegroundBed = foregroundBedPath, genome = "testgenome")


[Package enrichTF version 1.0.0 Index]