annotFeaturesComp: Features annotation

In bitona/MineICA: Analysis of an ICA decomposition obtained on genomics data

Features annotation

Description

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

Usage

  annotFeaturesComp(icaSet, params,
    type = toupper(typeID(icaSet)["geneID_annotation"]),
    featureId = typeID(icaSet)["featureID_biomart"],
    geneId = typeID(icaSet)["geneID_biomart"])

Arguments

icaSet	An object of class IcaSet whose features have to be annotated. The attribute annotation of this object contains the annotation package to be used.
params	An object of class MineICAParams containing the parameters of the analysis.
type	The ID of the object of the annotation package to be used for the annotation, must be available in ls("package:package_name")
featureId	The type of the feature IDs, in the biomaRt way (type listFilters(mart) to choose one). Used when annotation(icaSet) is of length 0.
geneId	The type of the gene IDs, in the biomaRt way (type listAttributes(mart) to choose one). Used when annotation(icaSet) is of length 0.

Details

This function is called by function annotInGene which will check the validity of the attributes annotation, typeID, chipManu and eventually chipVersion of icaSet. If available, the attribute annotation of argument icaSet must be an annotation package and will be used to annotate the featureNames of icaSet. If attribute annotation of argument icaSet is not available (of length 0), biomaRt is used to annotate the features.

This function fills the attributes SByGene and datByGene of the argument 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 projection values is used for attribute SByGene, and the median of 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.

Value

This function returns the argument icaSet with attributes SByGene and datByGene filled.

Author(s)

Anne Biton

See Also

annotFeatures, annotFeaturesWithBiomaRt, annotInGene

Examples

## load an example of IcaSet
data(icaSetCarbayo)
params <- buildMineICAParams()
require(hgu133a.db)
####===================================================
## Use of annotation package contained in annotation(icaSet)
####====================================================
## annotation in SYMBOL
icaSetCarbayo_annot <- annotFeaturesComp(icaSet=icaSetCarbayo, params=params, type="SYMBOL")
# arg 'type' is optional since the function uses contents of typeID(icaSet) as the defaults,
# it is specified in these examples for pedagogy views

## annotation in Entrez Gene
icaSetCarbayo_annot <- annotFeaturesComp(icaSet=icaSetCarbayo, params=params, type="ENTREZID")

## Not run: 
####===================================================
## Use of biomaRt, when annotation(icaSet) is of length 0
####====================================================
## empty attribute 'annotation' of the IcaSet object
# when this attribute is not specified, biomaRt is used for annotation
annotation(icaSetCarbayo) <- character()

# make sure the mart attribute is correctly defined
mart(icaSetCarbayo) <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

## make sure elements "featureID_biomaRt" and "geneID_biomaRt" of typeID(icaSet) are correctly filled
# they will be used by function 'annotFeaturesComp' through biomaRt to query the database
typeID(icaSetCarbayo)

## run annotation of HG-U133A probe set IDs into Gene Symbols using biomaRt
icaSetCarbayo_annot <- annotFeaturesComp(icaSet=icaSetCarbayo, params=params)


## End(Not run)

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.