addGeneInfo: Utility Function to Add Annotation to existing ExpressionSet...

In a4Preproc: Automated Affymetrix Array Analysis Preprocessing Package

Description

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

Usage

addGeneInfo(eset, annotationLibrary = NULL)

Arguments

eset	ExpressionSet object for to which one wants to add additional annotation information
annotationLibrary	Annotation Library to use. Must be specified when working with Entrez gene IDs. In this case, one can make use of the JnJ annotation packages such as hgu133plus2hsentrezgJnJ. If not specified, the annotation of the package will be automatically requested with annotation() of the expressionSet object eset and then Affymetrix probe set IDs are expected in featureNames

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`)

Example output

Loading required package: Biobase
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, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: hgu95av2.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: org.Hs.eg.db


NULL

a4Preproc documentation built on Nov. 8, 2020, 5:07 p.m.