Hypergeometric Tests for MeSH term association

Description

Given a MeSHHyperGParams object containing a set of selected and background gene IDs, and gene-MeSH annotation data of interest, meshHyperGTest performs Hypergeomtric test for over-representation of each MeSH term accouting for the multiple testing correction.

Arguments

Details

For details on creating MeSHHyperGParams object, please read the documentation in the MeSHHyperGParams-class.

Value

A MeSHHyperGResult object.

Author(s)

Gota Morota, Koki Tsuyuzaki, Takeru Nakazato, Itoshi Nikaido

Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>

See Also

meshr-package, MeSHHyperGParams-class, MeSHHyperGResult-class

Examples

data(geneid.cummeRbund)
data(sig.geneid.cummeRbund)

meshParams <- new("MeSHHyperGParams", geneIds=sig.geneid.cummeRbund[,2], universeGeneIds=geneid.cummeRbund[,2], annotation="MeSH.Hsa.eg.db", category="Z", database="gene2pubmed", pvalueCutoff=0.05, pAdjust="none")

meshR <- meshHyperGTest(meshParams)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(meshr)
Loading required package: fdrtool
Loading required package: Category
Loading required package: stats4
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: AnnotationDbi
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: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: cummeRbund
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

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

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

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

    promoters

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

    promoters

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

    samples

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

    conditions

Loading required package: org.Hs.eg.db

Loading required package: MeSH.db
Loading required package: MeSHDbi

Attaching package: 'MeSHDbi'

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

    packageName

Loading required package: MeSH.AOR.db
Loading required package: MeSH.PCR.db
Loading required package: MeSH.Hsa.eg.db
Loading required package: MeSH.Aca.eg.db
Loading required package: MeSH.Bsu.168.eg.db
Loading required package: MeSH.Syn.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/meshr/meshHyperGTest.Rd_%03d_medium.png", width=480, height=480)
> ### Name: meshHyperGTest
> ### Title: Hypergeometric Tests for MeSH term association
> ### Aliases: meshHyperGTest meshHyperGTest,MeSHHyperGParams-method
> ### Keywords: models
> 
> ### ** Examples
> 
> data(geneid.cummeRbund)
> data(sig.geneid.cummeRbund)
> 
> meshParams <- new("MeSHHyperGParams", geneIds=sig.geneid.cummeRbund[,2], universeGeneIds=geneid.cummeRbund[,2], annotation="MeSH.Hsa.eg.db", category="Z", database="gene2pubmed", pvalueCutoff=0.05, pAdjust="none")
> 
> meshR <- meshHyperGTest(meshParams)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>