annotFeaturesWithBiomaRt: Annotation of features using 'biomaRt'

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

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)
}

Example output

Loading required package: BiocGenerics
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Attaching package: 'BiocGenerics'

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    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
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MineICA documentation built on Nov. 8, 2020, 5:35 p.m.