get_annotation: Get an annotation data frame from biomaRt

In bioinfo-pf-curie/bioshiny-modules-library: This library aims to provide R shiny apps developers of the Institut Curie with different modules witch can be used as bricks to build bigger shiny app

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)

bioinfo-pf-curie/bioshiny-modules-library documentation built on Dec. 19, 2021, 9:45 a.m.