FRiPQC: Quality control for fraction of reads in peaks (FRiP)

In wzthu/wzzw: An Easy-to-use Systematic pipeline for ATACseq data analysis

Quality control for fraction of reads in peaks (FRiP)

Description

Calculate the fraction of reads falling within peak regions

Usage

atacFripQC(
  atacProc,
  atacProcPeak = NULL,
  bsgenome = NULL,
  reportOutput = NULL,
  readsBedInput = NULL,
  peakBedInput = NULL,
  ...
)

## S4 method for signature 'ATACProc'
atacFripQC(
  atacProc,
  atacProcPeak = NULL,
  bsgenome = NULL,
  reportOutput = NULL,
  readsBedInput = NULL,
  peakBedInput = NULL,
  ...
)

fripQC(readsBedInput, peakBedInput, bsgenome = NULL, reportOutput = NULL, ...)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacSamToBed samToBed atacBedUtils bedUtils
atacProcPeak	ATACProc-class object scalar. It has to be the return value of upstream process: atacPeakCalling, peakCalling.
bsgenome	BSGenome object scalar. BSGenome object for specific species.
reportOutput	Character scalar. The report file path
readsBedInput	Character scalar. Reads BED file for peak calling.
peakBedInput	Character scalar. Peaks BED file
...	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, or you can use fripQC instead.

Value

An invisible fripQC object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacSamToBed atacBedUtils

Examples

library(R.utils)
library(BSgenome.Hsapiens.UCSC.hg19)
library(magrittr)
td <- tempdir()
setTmpDir(td)

bedbzfile <- system.file(package="esATAC", "extdata", "chr20.50000.bed.bz2")
bedfile <- file.path(td,"chr20.50000.bed")
bunzip2(bedbzfile,destname=bedfile,overwrite=TRUE,remove=FALSE)

bedUtils(bedInput = bedfile,maxFragLen = 100, chrFilterList = NULL)  %>%
atacPeakCalling %>% atacFripQC(bsgenome=BSgenome.Hsapiens.UCSC.hg19)


dir(td)

wzthu/wzzw documentation built on Aug. 13, 2022, 7:11 a.m.