annotateFromBiomart {yarn} | R Documentation

## Annotate your Expression Set with biomaRt

### Description

Annotate your Expression Set with biomaRt

### Usage

    annotateFromBiomart(obj, genes = featureNames(obj),
      filters = "ensembl_gene_id", attributes = c("ensembl_gene_id",
      "hgnc_symbol", "chromosome_name", "start_position", "end_position"),
      biomart = "ensembl", dataset = "hsapiens_gene_ensembl", ...)

### Arguments

`obj` | ExpressionSet object.
`genes` | Genes or rownames of the ExpressionSet.
`filters` | getBM filter value, see getBM help file.
`attributes` | getBM attributes value, see getBM help file.
`biomart` | BioMart database name you want to connect to. Possible database names can be retrieved with teh function listMarts.
`dataset` | Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart('ensembl'), followed by listDatasets(mart).
`...` | Values for useMart, see useMart help file.

### Value

ExpressionSet object with a fuller featureData.

### Examples

    data(skin)
    # subsetting and changing column name just for a silly example
    skin <- skin[1:10,]
    colnames(fData(skin)) = paste("names",1:6)
    biomart<-"ENSEMBL_MART_ENSEMBL";
    genes <- sapply(strsplit(rownames(skin),split="\\."),function(i)i[1])
    newskin <-annotateFromBiomart(skin,genes=genes,biomar=biomart)
    head(fData(newskin)[,7:11])

[Package yarn version 1.12.0 Index]