GSEAresultTable: Form a table for GSEA results

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

Description

Form a table for GSEA results.

Usage

GSEAresultTable(gene.set, GSDesc = FALSE)

Arguments

gene.set	a SeqGeneSet object after running GSEnrichAnalyze.
GSDesc	logical indicating whether to output gene set descriptions. default: FALSE

Value

A data frame containing columns of GSName, GSSize, ES, ES.pos, pval, FDR, and FWER.

Author(s)

Xi Wang, [e-mail]

See Also

GSEnrichAnalyze, topGeneSets

Examples

data(DEscore, package="SeqGSEA")
data(DSscore, package="SeqGSEA")
gene.score <- geneScore(DEscore, DSscore, method="linear", DEweight = 0.3)
data(DEscore.perm, package="SeqGSEA")
data(DSscore.perm, package="SeqGSEA")
gene.score.perm <- genePermuteScore(DEscore.perm, DSscore.perm, method="linear",  DEweight=0.3)
data(GS_example, package="SeqGSEA")
GS_example <- GSEnrichAnalyze(GS_example, gene.score, gene.score.perm)
head(GSEAresultTable(GS_example))

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:
executing %dopar% sequentially: no parallel backend registered 
                GSName GSSize        ES ES.pos pval FDR FWER
1        ERB2_UP.V1_DN      6 0.9322128     11 0.62   1    1
2 AKT_UP_MTOR_DN.V1_UP      6 0.2393357    165 0.99   1    1
3         AKT_UP.V1_UP      6 0.5976466    108 0.88   1    1
4      ATF2_S_UP.V1_UP      5 0.2478502    142 0.93   1    1
5        PKCA_DN.V1_DN      5 0.8234479    101 0.71   1    1
6        PTEN_DN.V2_DN      5 0.7906115     56 0.72   1    1

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