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 2.8.1 Index]