DEpermutePval: Permutation for p-values in differential expression analysis

In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

Calculate permutation p-values in differential expression analysis for each genes.

Usage

DEpermutePval(DEGres, permuteNBstat)

Arguments

DEGres	the output of DENBStat4GSEA.
permuteNBstat	the output of DENBStatPermut4GSEA.

Value

A data frame containing the expression means and variances for each gene in each group compared, and NB-stats, permutation p-values and adjusted p-values for each gene.

Author(s)

Xi Wang, [e-mail]

See Also

runDESeq, DENBStat4GSEA, DENBStatPermut4GSEA, DENBTest

Examples

data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)
DEGres <- DENBStat4GSEA(DEG)
DEpermNBstat <- DENBStatPermut4GSEA(DEG, permuteMat)
DEGres <- DEpermutePval(DEGres, DEpermNBstat) 
head(DEGres)

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.
There were 11 warnings (use warnings() to see them)
                             id  baseMeanA       VarA  baseMeanB        VarB
ENSG00000000003 ENSG00000000003 471.776901 796.254809 429.875533 2439.206997
ENSG00000000005 ENSG00000000005   4.908256   5.105466   6.670875    7.304415
ENSG00000000419 ENSG00000000419 210.128418 446.421084 204.279787 1034.045306
ENSG00000000457 ENSG00000000457 146.952274  93.502104 103.711129   36.902680
ENSG00000000460 ENSG00000000460  63.235236  34.274908  52.389336   49.145628
ENSG00000000938 ENSG00000000938  57.554003  36.902713 154.359623 4227.252000
                    NBstat perm.pval perm.padj
ENSG00000000003  0.5426504       0.5         1
ENSG00000000005  0.2503510       0.5         1
ENSG00000000419  0.0231052       1.0         1
ENSG00000000457 14.3384053       0.0         0
ENSG00000000460  1.4101270       0.3         1
ENSG00000000938  2.1976989       0.0         0

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.