runDESeq: Run DESeq for differential expression analysis

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/DEscore.R

Description

This function provides a wrapper to run DESeq for differential expression analysis. It includes two steps, DESeq::estimateSizeFactors and DESeq::estimateDispersions.

Usage

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runDESeq(geneCounts, label)

Arguments

geneCounts

a matrix containing read counts for each gene, can be the output of getGeneCount.

label

the sample classification labels.

Value

A CountDataSet object with size factors and dispersion parameters been estimated.

Author(s)

Xi Wang, [email protected]

References

Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data, Genome Biol, 11, R106.

See Also

getGeneCount, DENBTest, DENBStat4GSEA

Examples

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data(RCS_example, package="SeqGSEA")
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)

Example output

Loading required package: Biobase
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

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

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
Warning message:
In .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning message:
system call failed: Cannot allocate memory 

SeqGSEA documentation built on Nov. 17, 2017, 9:49 a.m.