get_annotation: Get an annotation data frame from biomaRt

In pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach

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)

pcaExplorer documentation built on Nov. 8, 2020, 5:29 p.m.