A toy example of a list of gene identifiers and the respective p-values

Description

The geneList data is compiled from a differential expression analysis of the ALL dataset. It contains just a small number of genes with the corespondent p-values. The information on where to find the GO annotations is stored in the ALL object.

The topDiffGenes function included in this dataset will select the differentially expressed genes, at 0.01 significance level, from geneList.

Usage

data(geneList)

Source

Generated using the ALL gene expression data. See the "scripts" directory.

Examples

data(geneList)

## print the object
head(geneList)
length(geneList)

## the number of genes with a p-value less than 0.01
sum(topDiffGenes(geneList))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/geneList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geneList
> ### Title: A toy example of a list of gene identifiers and the respective
> ###   p-values
> ### Aliases: geneList topDiffGenes affyLib
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(geneList)
> 
> ## print the object
> head(geneList)
1095_s_at   1130_at   1196_at 1329_s_at 1340_s_at 1342_g_at 
1.0000000 1.0000000 0.6223795 0.5412240 1.0000000 1.0000000 
> length(geneList)
[1] 323
> 
> ## the number of genes with a p-value less than 0.01
> sum(topDiffGenes(geneList))
[1] 50
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>