annotFeaturesWithBiomaRt {MineICA} | R Documentation

## Annotation of features using `biomaRt`

### Description

This function annotates a set of features using `biomaRt`

### Usage

      annotFeaturesWithBiomaRt(features, featureId, geneId,
        mart = useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl"))

### Arguments

`features` | Feature IDs to be annotated
`featureId` | The type of the feature IDs, in the `biomaRt` way (type `listFilters(mart)` to choose one)
`geneId` | The type of the gene IDs, in the `biomaRt` way (type `listAttributes(mart)` to choose one)
`mart` | The mart object (database and dataset) used for annotation, see function `useMart` of package `biomaRt`

### Value

A vector of gene IDs indexed by the feature IDs.

### Author(s)

Anne Biton

### Examples

    if (interactive()) {
    # define the database to be queried by biomaRt
    mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

    # annotate a set of HG-U133a probe sets IDs into Gene Symbols
    annotFeaturesWithBiomaRt(features = c("1007_s_at", "1053_at", "117_at", "121_at", "1255_g_at"),
    featureId="affy_hg_u133a", geneId="hgnc_symbol", mart=mart)

    # annotate a set of Ensembl Gene IDs into Gene Symbols
    annotFeaturesWithBiomaRt(features = c("ENSG00000101412", "ENSG00000112242",
                                          "ENSG00000148773", "ENSG00000131747", "ENSG00000170312",
                                          "ENSG00000117399"), featureId="ensembl_gene_id", geneId="hgnc_symbol", mart=mart)
    }

[Package MineICA version 1.22.0 Index]