PeakQC: Quality control for peak overlap

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

Quality control for peak overlap

Description

These functions are used to calculate the overlap ratio in specific quality control rigion. Blacklist and DHS region are provided. You can also set your own BED file as quality control rigion.

Usage

atacPeakQC(
  atacProc,
  bsgenome = NULL,
  reportOutput = NULL,
  qcbedInput = c("DHS", "blacklist", "path/to/bed"),
  bedInput = NULL,
  newStepType = "PeakQC",
  ...
)

## S4 method for signature 'ATACProc'
atacPeakQC(
  atacProc,
  bsgenome = NULL,
  reportOutput = NULL,
  qcbedInput = c("DHS", "blacklist", "path/to/bed"),
  bedInput = NULL,
  newStepType = "PeakQC",
  ...
)

peakQC(
  bedInput,
  bsgenome = NULL,
  reportOutput = NULL,
  qcbedInput = c("DHS", "blacklist", "path/to/bed"),
  newStepType = "PeakQC",
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacSamToBed, atacBedUtils.
bsgenome	BSGenome object scalar. BSGenome object for specific species.
reportOutput	Character scalar. The report file path.
qcbedInput	Character scalar. It can be "DHS","blacklist" or Other quality control BED file input path.
bedInput	Character scalar. BED file input path for quality control.
newStepType	Character scalar. New step type name for different default parameters.
...	Additional arguments, currently unused.

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object 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 peakQC instead.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacSamToBed atacBedUtils

Examples

library(R.utils)
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)
blacklistfile <- system.file(package="esATAC", "extdata", "hg19.blacklist.bed")
library(BSgenome.Hsapiens.UCSC.hg19)
bedUtils(bedInput = bedfile,maxFragLen = 100, chrFilterList = NULL) %>%
atacPeakCalling %>% atacPeakQC(qcbedInput = blacklistfile, bsgenome = BSgenome.Hsapiens.UCSC.hg19)
dir(td)

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.