Convert genes to symbols

Convert genes to symbols

Usage

convertGenesToSymbols(object, ...)

convertSymbolsToGenes(object, ...)

# S4 method for SummarizedExperiment
convertGenesToSymbols(object, strict = FALSE)

# S4 method for SummarizedExperiment
convertSymbolsToGenes(object, strict = FALSE)

Arguments

object

Object.

strict

logical(1). Require that all identifiers contain gene name (symbol) metadata stored in the object. Disabled by default, to support objects containing custom gene identifiers, such as FASTA spike-ins.

...

Additional arguments.

Value

Modified object of same class.

Note

Updated 2021-10-21.

Examples

data(RangedSummarizedExperiment, package = "AcidTest")

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
x <- convertGenesToSymbols(object)
print(x)
#> class: RangedSummarizedExperiment 
#> dim: 500 12 
#> metadata(3): version date interestingGroups
#> assays(1): counts
#> rownames(500): TSPAN6 TNMD ... ABCF2 CHPF2
#> rowData names(10): broadClass description ... ncbiGeneId seqCoordSystem
#> colnames(12): sample01 sample02 ... sample11 sample12
#> colData names(1): condition
## Interconvert back to gene IDs.
y <- convertSymbolsToGenes(x)
print(y)
#> class: RangedSummarizedExperiment 
#> dim: 500 12 
#> metadata(3): version date interestingGroups
#> assays(1): counts
#> rownames(500): ENSG00000000003.15 ENSG00000000005.6 ...
#>   ENSG00000033050.9 ENSG00000033100.16
#> rowData names(10): broadClass description ... ncbiGeneId seqCoordSystem
#> colnames(12): sample01 sample02 ... sample11 sample12
#> colData names(1): condition