Map genes — mapGenesToRownames • AcidExperiment

Take a user-defined gene vector and dynamically map the input to either the object rownames or the gene names (symbols). These functions are useful for writing code that needs to handle either gene identifier or gene name input dynamically (e.g. for single-cell RNA-seq marker analysis).

Usage

mapGenesToRownames(object, ...)

mapGenesToIds(object, ...)

mapGenesToSymbols(object, ...)

# S4 method for class 'SummarizedExperiment'
mapGenesToRownames(object, genes, strict = TRUE)

# S4 method for class 'SummarizedExperiment'
mapGenesToIds(object, genes, strict = TRUE)

# S4 method for class 'SummarizedExperiment'
mapGenesToSymbols(object, genes, strict = TRUE)

Arguments

object: Object.
genes: character. Gene identifiers.
strict: logical(1). Require all genes to match. Recommended by default. If set FALSE, instead will return a warning to the user, and subset the genes vector to only include matches.
...: Additional arguments.

Value

character.

Note

Updated 2021-10-08.

Ambiguous gene names

Some genomes (e.g. Homo sapiens, Mus musculus) contain duplicated gene names for multiple gene identifiers. Normally we handle these ambiguous gene names by sanitizing them with make.names. If a user requests a gene name that is duplicated, these functions will return a warning.

Examples

data(RangedSummarizedExperiment, package = "AcidTest")

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
rownames <- head(rownames(object))
print(rownames)
#> [1] "gene001" "gene002" "gene003" "gene004" "gene005" "gene006"
g2s <- GeneToSymbol(object)
geneIds <- head(g2s[["geneId"]])
print(geneIds)
#> [1] "ENSG00000000003.15" "ENSG00000000005.6"  "ENSG00000000419.12"
#> [4] "ENSG00000000457.14" "ENSG00000000460.17" "ENSG00000000938.13"
geneNames <- head(g2s[["geneName"]])
print(geneNames)
#> [1] "TSPAN6"   "TNMD"     "DPM1"     "SCYL3"    "C1orf112" "FGR"     

## Row names.
mapGenesToRownames(object, genes = rownames)
#>   gene001   gene002   gene003   gene004   gene005   gene006 
#> "gene001" "gene002" "gene003" "gene004" "gene005" "gene006" 
mapGenesToRownames(object, genes = geneIds)
#> ENSG00000000003.15  ENSG00000000005.6 ENSG00000000419.12 ENSG00000000457.14 
#>          "gene001"          "gene002"          "gene003"          "gene004" 
#> ENSG00000000460.17 ENSG00000000938.13 
#>          "gene005"          "gene006" 
mapGenesToRownames(object, genes = geneNames)
#>    TSPAN6      TNMD      DPM1     SCYL3  C1orf112       FGR 
#> "gene001" "gene002" "gene003" "gene004" "gene005" "gene006" 

## Gene identifiers.
mapGenesToIds(object, genes = rownames)
#>              gene001              gene002              gene003 
#> "ENSG00000000003.15"  "ENSG00000000005.6" "ENSG00000000419.12" 
#>              gene004              gene005              gene006 
#> "ENSG00000000457.14" "ENSG00000000460.17" "ENSG00000000938.13" 
mapGenesToIds(object, genes = geneIds)
#>   ENSG00000000003.15    ENSG00000000005.6   ENSG00000000419.12 
#> "ENSG00000000003.15"  "ENSG00000000005.6" "ENSG00000000419.12" 
#>   ENSG00000000457.14   ENSG00000000460.17   ENSG00000000938.13 
#> "ENSG00000000457.14" "ENSG00000000460.17" "ENSG00000000938.13" 
mapGenesToIds(object, genes = geneNames)
#>               TSPAN6                 TNMD                 DPM1 
#> "ENSG00000000003.15"  "ENSG00000000005.6" "ENSG00000000419.12" 
#>                SCYL3             C1orf112                  FGR 
#> "ENSG00000000457.14" "ENSG00000000460.17" "ENSG00000000938.13" 

## Gene names (symbols).
mapGenesToSymbols(object, genes = rownames)
#>    gene001    gene002    gene003    gene004    gene005    gene006 
#>   "TSPAN6"     "TNMD"     "DPM1"    "SCYL3" "C1orf112"      "FGR" 
mapGenesToSymbols(object, genes = geneIds)
#> ENSG00000000003.15  ENSG00000000005.6 ENSG00000000419.12 ENSG00000000457.14 
#>           "TSPAN6"             "TNMD"             "DPM1"            "SCYL3" 
#> ENSG00000000460.17 ENSG00000000938.13 
#>         "C1orf112"              "FGR" 
mapGenesToSymbols(object, genes = geneNames)
#>     TSPAN6       TNMD       DPM1      SCYL3   C1orf112        FGR 
#>   "TSPAN6"     "TNMD"     "DPM1"    "SCYL3" "C1orf112"      "FGR"