FastQC {esATAC} | R Documentation

## 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)

[Package esATAC version 1.2.3 Index]