% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/get_annotation.R
 \name{get_annotation}
 \alias{get_annotation}
 \title{Get an annotation data frame from biomaRt}
 \usage{
 get_annotation(dds, biomart_dataset, idtype)
 }
 \arguments{

 \item{dds}{A \code{\link[=DESeqDataSet]{DESeqDataSet()}} object}

 
 \item{biomart_dataset}{A biomaRt dataset to use. To see the list, type
 \code{mart = useMart('ensembl')}, followed by \code{listDatasets(mart)}.}
 
 \item{idtype}{Character, the ID type of the genes as in the row names of

 \code{dds}, to be used for the call to \code{\link[=getBM]{getBM()}}}

 }

 \value{
 A data frame for ready use in \code{pcaExplorer}, retrieved from biomaRt.
 }

 \description{
 Get an annotation data frame from biomaRt
 }

 \examples{

 library("airway")
 data("airway", package = "airway")

 airway
 dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                              colData = colData(airway),

                                              design = ~dex+cell)

 \dontrun{

 get_annotation(dds_airway, "hsapiens_gene_ensembl", "ensembl_gene_id")

 }
 }