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Last data update: 2014.03.03

R: Main Rqc function

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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Rqc)
Loading required package: BiocParallel
Loading required package: ShortRead
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rqc/rqc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rqc
> ### Title: Main Rqc function
> ### Aliases: rqc
> ### Keywords: graphics qc
> 
> ### ** 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)
'/tmp/RtmpFJXSC0/rqc_report.html' has been created.
Warning message:
closing unused connection 3 (/home/ddbj/local/lib64/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz) 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>