FastQC: Quality control for ATAC-seq data.

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

Quality control for ATAC-seq data.

Description

Generate quality control plots from fastq of ATAC-seq data.

Usage

atacQCReport(atacProc, input_file = NULL, output_file = NULL, ...)

## S4 method for signature 'ATACProc'
atacQCReport(atacProc, input_file = NULL, output_file = NULL, ...)

qcreport(input_file, output_file = NULL, ...)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacUnzipAndMerge, atacRenamer
input_file	Character scalar. Input file path. One or more(vector) fastq file path.
output_file	Character scalar. output file path. Defult:"input_file_QC.pdf" in the same folder as your input file.
...	Additional arguments, currently unused.

Details

Every highthroughput sequencing need quality control analysis, this function provide QC for ATAC-seq, such as GC content.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Wei Zhang

See Also

atacUnzipAndMerge, atacRenamer

Examples

library(R.utils)
fra_path <- system.file("extdata", "chr20_1.2.fq.bz2", package="esATAC")
fq1 <- as.vector(bunzip2(filename = fra_path,
destname = file.path(getwd(), "chr20_1.fq"),
ext="bz2", FUN=bzfile, overwrite=TRUE, remove = FALSE))
fra_path <- system.file("extdata", "chr20_2.2.fq.bz2", package="esATAC")
fq2 <- as.vector(bunzip2(filename = fra_path,
destname = file.path(getwd(), "chr20_2.fq"),
ext="bz2", FUN=bzfile, overwrite=TRUE, remove = FALSE))
## Not run: 
qcreport(input_file = c(fq1, fq2))

## End(Not run)

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