get_annotation_orgdb {pcaExplorer} | R Documentation

## Get an annotation data frame from org db packages

### 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)

[Package pcaExplorer version 2.20.2 Index]