Utility Function to Add Annotation to existing ExpressionSet Objects

Description

Adds appropriate featureData, similar to the metadata added in the pipeline script, to the ExpressionSet object.

Usage

addGeneInfo(eset, annotationLibrary = NULL)

Arguments

Details

Slots of featureData(a4ALL) are

• Entrez ID~: Entrez ID as retrieved from annotation package

• Ensembl ID~: Ensembl ID as retrieved from annotation package

• Gene Symbol~: Gene symbol as retrieved from annotation package

• Description~: Description as retrieved from annotation package

Value

a new ExpressionSet object with the additional information stored as feature data

Note

One should always use subscripting of featureData by column name (e.g. featureData(a4ALL)$`Entrez ID`; as the pipeline ExpressionSets have one additional column compared to the ExpressionSet objects produced by addGeneInfo, i.e. column 2 of the pipeline ExpressionSets corresponds to column one of an addGeneInfo ExpressionSet.

Author(s)

Tobias Verbeke, Steven Osselaer

Examples

  library(ALL)
  data(ALL)
  a4ALL <- addGeneInfo(ALL)
  head(featureData(a4ALL)$`Entrez ID`)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(a4Preproc)
Loading required package: AnnotationDbi
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: 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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Preproc/addGeneInfo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addGeneInfo
> ### Title: Utility Function to Add Annotation to existing ExpressionSet
> ###   Objects
> ### Aliases: addGeneInfo
> ### Keywords: manip
> 
> ### ** Examples
> 
>   library(ALL)
>   data(ALL)
>   a4ALL <- addGeneInfo(ALL)
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


>   head(featureData(a4ALL)$`Entrez ID`)
NULL
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>