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Last data update: 2014.03.03

R: A parallel version of DEXUS.

dexus.parallel

R Documentation

A parallel version of DEXUS.

Description

Speeds up DEXUS by using multiple processors. Uses the parallel package to parallelize a DEXUS call.

Usage

  dexus.parallel(X, ncores = 2, normalization = "RLE",
    ignoreIfAllCountsSmaller = 1, resultObject = "S4", ...)

Arguments

`X`	Either a vector of counts or a raw data matrix, where columns are interpreted as samples and rows as genomic regions.
`ncores`	The number of cores (CPUs) that will be used by the parallelization.
`normalization`	Normalization method to be used. (Default="RLE")
`ignoreIfAllCountsSmaller`	A transcript is considered as not expressed if all counts are smaller than the given value. (Default=1)
`resultObject`	Type of the result object; can either be a list ("list") or an instance of "DEXUSResult" ("S4"). (Default="S4").
`...`	Other options to be passed to `dexus()`.

Value

"list"

Author(s)

Guenter Klambauer klambauer@bioinf.jku.at and Thomas Unterthiner unterthiner@bioinf.jku.at

Examples

data(dexus)
result <- dexus.parallel(countsPickrell[1:10, ],ncores=1)

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(dexus)
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


Attaching package: 'dexus'

The following object is masked from 'package:BiocGenerics':

    sizeFactors

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dexus/dexus.parallel.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dexus.parallel
> ### Title: A parallel version of DEXUS.
> ### Aliases: dexus.parallel
> 
> ### ** Examples
> 
> data(dexus)
> result <- dexus.parallel(countsPickrell[1:10, ],ncores=1)
Switching to single-threaded code.
Filtered out 0 % of the genes due to low counts
Unsupervised mode.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>