PECA_TF_enrich {enrichTF} | R Documentation |
This is a pipeline for TF enrichment with PECA model.
PECA_TF_enrich(inputForegroundBed, genome, threads = 2, ...)
inputForegroundBed |
|
genome |
|
threads |
|
... |
Additional arguments to set arguments for each Steps. See below for 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.
An invisible list
contains all four steps
EnrichTF
objects
Zheng Wei
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
foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed") # This is the whole pipeline example. PECA_TF_enrich(inputForegroundBed = foregroundBedPath, genome = "testgenome")