Enrichment analysis for MeSH terms.

Description

meshr package conducts a MeSH enrichment analysis employing gene-MeSH annotation data. A hypergeometric test accounting for a multiple tesing correction is used to find significantly enriched MeSH terms.

Details

Index:

meshHyperGTest performs a hypergeometric statistical test.

Further information is available in the vignettes.

Author(s)

Gota Morota, Koki Tsuyuzaki, Takeru Nakazato, Itoshi Nikaido

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

See Also

MeSHHyperGParams-class, MeSHHyperGResult-class, meshHyperGTest

Examples

ls("package:meshr")

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(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/meshr-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: meshr-package
> ### Title: Enrichment analysis for MeSH terms.
> ### Aliases: meshr-package meshr
> ### Keywords: package
> 
> ### ** Examples
> 
> ls("package:meshr")
 [1] "annotation"        "annotation<-"      "category"         
 [4] "category<-"        "database"          "database<-"       
 [7] "geneIds"           "initialize"        "makeValidParams"  
[10] "meshAnnotation"    "meshCategory"      "meshDatabase"     
[13] "meshHyperGTest"    "meshIds"           "pAdjust"          
[16] "pAdjust<-"         "pvalueCutoff"      "pvalueCutoff<-"   
[19] "save.pdf"          "show"              "summary"          
[22] "universeGeneIds"   "universeGeneIds<-"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>