get_annotation {pcaExplorer} | R Documentation

## Get an annotation data frame from biomaRt

### Description

Get an annotation data frame from biomaRt

### Usage

    get_annotation(dds, biomart_dataset, idtype)

### Arguments

`dds` | A `DESeqDataSet` object
`biomart_dataset` | A biomaRt dataset to use. To see the list, type `mart = useMart('ensembl')`, followed by `listDatasets(mart)`.
`idtype` | Character, the ID type of the genes as in the row names of `dds`, to be used for the call to `getBM`

### Value

A data frame for ready use in `pcaExplorer`, retrieved from biomaRt.

### Examples

    library(airway)
    data(airway)
    airway
    dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                                 colData = colData(airway),
                                                 design = ~dex+cell)
    ## Not run:
    get_annotation(dds_airway, "hsapiens_gene_ensembl", "ensembl_gene_id")

    ## End(Not run)

[Package pcaExplorer version 2.20.2 Index]