get_annotation_orgdb: Get an annotation data frame from org db packages

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

Description

Get an annotation data frame from org db packages

Usage

get_annotation_orgdb(dds, orgdb_species, idtype)

Arguments

dds	A DESeqDataSet object
orgdb_species	Character string, named as the org.XX.eg.db package which should be available in Bioconductor
idtype	Character, the ID type of the genes as in the row names of dds, to be used for the call to mapIds

Value

A data frame for ready use in pcaExplorer, retrieved from the org db packages

Examples

library(airway)
data(airway)
airway
dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                             colData = colData(airway),
                                             design = ~dex+cell)
## Not run: 
get_annotation_orgdb(dds_airway, "org.Hs.eg.db", "ENSEMBL")

## End(Not run)

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