rqc {Rqc} | R Documentation

## 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.

### Author(s)

Welliton Souza

### 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)

[Package Rqc version 1.26.0 Index]