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]