Rqc (version 1.6.2)

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

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.

Details

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

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)