annotFeaturesComp {MineICA} | R Documentation

## 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)

[Package MineICA version 1.30.0 Index]