Convenient function to compute p-values from a gene expression matrix.

Description

Warping function of "mt.teststat", for computing p-values of a gene expression matrix.

Usage

   getPvalues(edata, classlabel, test = "t", alternative = c("greater", "two.sided", "less")[1],
   genesID = NULL, correction = c("none", "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD",
   "BH", "BY")[8]) 

Arguments

Value

An named numeric vector of p-values.

Author(s)

Adrian Alexa

See Also

GOKSTest, groupStats-class, getSigGroups-methods

Examples

library(ALL)
data(ALL)

## discriminate B-cell from T-cell
classLabel <- as.integer(sapply(ALL$BT, function(x) return(substr(x, 1, 1) == 'T')))

## Differentially expressed genes
geneList <- getPvalues(exprs(ALL), classlabel = classLabel,
                       alternative = "greater", correction = "BY")

hist(geneList, 50)

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)

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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(topGO)
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: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
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: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/topGO/getPvalues.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getPvalues
> ### Title: Convenient function to compute p-values from a gene expression
> ###   matrix.
> ### Aliases: getPvalues
> ### Keywords: graphs
> 
> ### ** Examples
> 
> 
> library(ALL)
> data(ALL)
> 
> ## discriminate B-cell from T-cell
> classLabel <- as.integer(sapply(ALL$BT, function(x) return(substr(x, 1, 1) == 'T')))
> 
> ## Differentially expressed genes
> geneList <- getPvalues(exprs(ALL), classlabel = classLabel,
+                        alternative = "greater", correction = "BY")
Loading required package: multtest
> 
> hist(geneList, 50)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>