Pipelines {enrichTF} | R Documentation

## ready-to-use pipelines

### Description

There are two ready-to-use pipelines in this package. One is the pipeline mainly for TF enrichment with PECA model. The ohter is the pipeline is for gene regulation analysis including the first pipeline and other related analysis like openness and gene ontology analysis.

### Usage

    PECA_TF_enrich(inputForegroundBed, genome, threads = 2,
      pipeName = "pipe", ...)

    GeneReguPipe(inputForegroundBed, genome, threads = 2,
      pipeName = "pipe", ...)

### 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
`pipeName` | `Character` scalar or vector. Pipeline name.
`...` | 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` scalar. A list containing all objects that belongs to the pipeline.

### 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 1.2.3 Index]