Rqc (version 1.6.2)

rqc: Main Rqc function

Description

Rqc is an optimized tool designed for quality assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces an HTML report, which contains a set of high-resolution images that can be directly used on publications.

Usage

rqc(path = ".", pattern, sample = TRUE, n = 1e+06, group = NULL, top = 10, pair = NULL, outdir = tempdir(), file = "rqc_report", openBrowser = TRUE, workers = multicoreWorkers())

Arguments

path

directory path that contains input files.

pattern

a regex expression that macthes to input file names

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. By default, it reads 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).

outdir

output directory path. Is created a temporary directory by default.

file

output file name.

openBrowser

if TRUE opens report file on default Internet Browser.

workers

Number of parallel workers. Set 1 to serial. Default value from multicoreWorkers.

Value

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

See Also

rqcQA

Examples

  options(device.ask.default = FALSE)
  folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
  rqc(folder, ".fastq.gz", pair=c(1,1), workers=1, openBrowser=FALSE)