FragLenDistr: Quality control for fragment length distribution

In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

Description

These functions are used to generate fragment distribution plot. The fourier transform of fragment distribution will be calculated. Strength distribution around period at 10.4bp and 180bp will be shown in another two plots.

Usage

atacFragLenDistr(atacProc, reportPrefix = NULL, bedInput = NULL, ...)

## S4 method for signature 'ATACProc'
atacFragLenDistr(atacProc, reportPrefix = NULL, bedInput = NULL, ...)

fragLenDistr(bedInput, reportPrefix = NULL, ...)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacSamToBed samToBed atacBedUtils bedUtils
reportPrefix	Character scalar. The prefix of report files path.
bedInput	Character scalar. BED file input path.
...	Additional arguments, currently unused.

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object(atacProc) or generated based on known parameters if their values are default(e.g. NULL). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use fragLenDistr instead.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacSamToBed samToBed atacBedUtils bedUtils

Examples

library(R.utils)
td <- tempdir()
setTmpDir(td)

bedbzfile <- system.file(package="esATAC", "extdata", "chr20.50000.bed.bz2")
bedfile <- file.path(td,"chr20.50000.bed")
## Not run: 
bunzip2(bedbzfile,destname=bedfile,overwrite=TRUE,remove=FALSE)
fragLenDistr(bedfile)

## End(Not run)

dir(td)

esATAC documentation built on Nov. 8, 2020, 6:58 p.m.