Skip to contents

Convert data set by mapping to human orthologs

Usage

convertToHuman(object, ...)

# S4 method for 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)
#>  Homo sapiens (Ensembl 100) genome detected.
#> ! Returning unmodified.
#> DESeqAnalysis 0.6.8.9000; DESeq2 1.38.3
#> data:
#>   dim: 500 12 
#>   metadata(1): version
#>   assays(4): counts mu H cooks
#>   rownames(500): gene1 gene2 ... gene499 gene500
#>   rowData names(39): 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