Convert data set by mapping to human orthologs

Usage

convertToHuman(object, ...)

# S4 method for class 'DESeqAnalysis'
convertToHuman(object, map = NULL)

Arguments

object: Object.
map: DFrame, or NULL. Ortholog mappings data frame returned by mapHumanOrthologs(). Since this function depends on the BioMart API and has a tendancy to time out, we're allowing passthrough of a cached object here instead. If left NULL, then mapHumanOrthologs() will be called internally.
...: Additional arguments.

Value

Modified object. Features (i.e. rownames) will be remapped to human genes.

Note

Updated 2023-04-28.

Examples

data(deseq, package = "DESeqAnalysis")

## DESeqAnalysis ====
object <- deseq
convertToHuman(object)
#> ℹ Homo sapiens (Ensembl 100) genome detected.
#> ! Returning unmodified.
#> DESeqAnalysis 0.7.1; DESeq2 1.41.12
#> data:
#>   dim: 500 12 
#>   metadata(1): version
#>   assays(4): counts mu H cooks
#>   rownames(500): gene1 gene2 ... gene499 gene500
#>   rowData names(40): broadClass description ... deviance maxCooks
#>   colnames(12): sample1 sample2 ... sample11 sample12
#>   colData names(3): condition treatment sizeFactor
#> transformType: varianceStabilizingTransformation
#> resultsNames(2): condition_B_vs_A treatment_D_vs_C
#> alphaThreshold: 0.01
#> lfcShrinkType: apeglm