annotInGene: Features annotation of an object of class IcaSet.

Description

This function annotates the features of an IcaSet object and fills its attributes SByGene and datByGene.

Usage

annotInGene(icaSet, params, annot = TRUE)

Arguments

icaSet

An object of class IcaSet to be annotated, must contain a valid annotation attribute.

params

An object of class MineICAParams containing the parameters of the analysis.

annot

TRUE (default) if the IcaSet object must indeed be annotated

Value

The modified argument icaSet, with filled attributes SByGene and datByGene.

Details

When attribute annotation of icaSet is not specified (of length 0), biomaRt is used to annotate the features through function annotFeaturesWithBiomaRt.

When specified, attribute annotation of argument icaSet must be an annotation package and will be used to annotate the featureNames of icaSet. In addition, the attribute typeID (a vector) of argument icaSet must contain a valid element geneID_annotation that determines the object of the package to be used for the annotation, see IcaSet.

When argument annot is TRUE, this function fills the attributes SByGene and datByGene of icaSet. When several feature IDs are available for a same gene ID, the median value of the corresponding features IDs is attributed to the gene (the median of the projection values is used for attribute SByGene, and the median of the expression values is used for attribute datByGene).

When attribute chipManu of the argument icaSet is "illumina", the features are first converted into nuID using the package 'lumi*Mapping' and then annotated into genes. In that case, features can only be annotated in ENTREZID or SYMBOL. It means that typeID(icaSet)['geneID_annotation'] must be either 'ENTREZID' or 'SYMBOL'. You will need to annotate yourself the IcaSet object if you want to use different IDs.

Examples

Run this code

#load data
data(icaSetCarbayo)
require(hgu133a.db)

# run annotation of the features into gene Symbols as specified in 'typeID(icaSetCarbayo)["geneID_annotation"]',
# using package hgu133a.db as defined in 'annotation(icaSetMainz)'
icaSetCarbayo <- annotInGene(icaSet=icaSetCarbayo, params=buildMineICAParams())

## Not run: 
# #load data
# library(breastCancerMAINZ)
# data(mainz)
# #run ICA
# resJade <- runICA(X=exprs(mainz), nbComp=5, method = "JADE", maxit=10000)
# 
# #build params
# params <- buildMineICAParams(resPath="mainz/")
# 
# #build a new IcaSet object, omitting annotation of the features (runAnnot=FALSE)
# #but specifying the element "geneID_annotation" of argument 'typeID'
# icaSetMainz <- buildIcaSet(params=params, A=data.frame(resJade$A), S=data.frame(resJade$S),
#                              dat=exprs(mainz), pData=pData(mainz),
#                              annotation="hgu133a.db", typeID= c(geneID_annotation = "SYMBOL",
#                              geneID_biomart = "hgnc_symbol", featureID_biomart = "affy_hg_u133a"),
#                              chipManu = "affymetrix", runAnnot=FALSE,
#                              mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl"))
# 
# #Attributes SByGene is empty and attribute datByGene refers to assayData
# SByGene(icaSetMainz)
# head(datByGene(icaSetMainz))
# 
# # run annotation of the features into gene Symbols as specified in 'typeID(icaSetMainz)["geneID_annotation"]',
# # using package hgu133a.db as defined in 'annotation(icaSetMainz)'
# icaSetMainz <- annotInGene(icaSet=icaSetMainz, params=params)
# ## End(Not run)