rqcQA: Quality Assessment Rqc function

In labbcb/Rqc: Quality Control Tool for High-Throughput Sequencing Data

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)

labbcb/Rqc documentation built on Aug. 2, 2021, 8:43 a.m.