rqcQA {Rqc} | R Documentation

## Quality Assessment Rqc function

### Description

Process a set of files and returns a list of quality control data. Files must be FASTQ format, compressed or not.

### Usage

    rqcQA(
      x,
      sample = TRUE,
      n = 1e+06,
      group = rep("None", length(x)),
      top = 10,
      pair = seq_along(x),
      ...
    )

    ## S4 method for signature 'list'
    rqcQA(x, sample, n, group, top, pair, workers = multicoreWorkers())

    ## S4 method for signature 'character'
    rqcQA(
      x,
      sample = TRUE,
      n = 1e+06,
      group = rep("None", length(x)),
      top = 10,
      pair = seq_along(x),
      workers = multicoreWorkers()
    )

    ## S4 method for signature 'BamFile'
    rqcQA(x, sample, n, group, top, pair)

    ## S4 method for signature 'FastqFile'
    rqcQA(x, sample, n, group, top, pair)

### Arguments

`x` | input file(s)
`sample` | It reads a random sample from files if this parameter is TRUE.
`n` | Number of sequences to read from each input file. This represents sample size if 'sample' parameter is TRUE, if not represents the chunk size to read on each iteration. Default is read a sample of one million sequences from each input file.
`group` | group name for each input file.
`top` | number of top over-represented reads. Default is 10 reads.
`pair` | combination of files for paired-end reads. By default, all input files are treated as single-end. For paired-end, please define a vector of numbers where two index with the same value represent a pair. Examples, single-end `c(1,2,3,4)` and paired-end `c(1,1,2,2)`.
`...` | other parameters
`workers` | number of parallel workers

### Details

Input files are read using `FastStreamer` and `FastSampler` classes of `ShortRead` package. Process multiple files in parallel using `bplapply` function of `BiocParallel` package.

### Value

A named list of `RqcResultSet` objects, each one represents a file.

### Methods (by class)

- `list`: process a list of `FastqFile` and `BamFile` objects.

- `character`: automatically detects file format (using `detectFileFormat` function) of input files then process.

- `BamFile`: process only one BAM file.

- `FastqFile`: process only one FASTQ file.

### Author(s)

Welliton Souza

### See Also

`rqc`

### Examples

    checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), {
      folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
      files <- list.files(full.names=TRUE, path=folder)
      rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1)
    }, keep="rqcResultSet")
    rqcReadQualityPlot(rqcResultSet)

[Package Rqc version 1.28.0 Index]