Fetch all genes

Fetch names/identifiers for all genes.

fetchAllGenes(species, types = c("symbol", "entrez", "ensembl"), config = NULL)

Arguments

species

String specifying the taxonomy ID of the species of interest.

types

Character vector specifying the types of gene names/identifiers to return. This is typically one or more of "symbol", "entrez", and "ensembl".

config

Configuration list, typically created by newConfig. If NULL, the default configuration is used.

Value

Data frame where each row represents a gene. Each column corresponds to one of the types and is a list of character vectors. Each vector contains names/identifiers of the specified type for each gene.

Author

Aaron Lun

Examples

out <- fetchAllGenes("9606")
head(out)
#>     symbol entrez      ensembl
#> 1     A1BG      1 ENSG0000....
#> 2      A2M      2 ENSG0000....
#> 3    A2MP1      3 ENSG0000....
#> 4     NAT1      9 ENSG0000....
#> 5     NAT2     10 ENSG0000....
#> 6 SERPINA3     12 ENSG0000....
head(out$symbol)
#> [[1]]
#> [1] "A1BG"
#> 
#> [[2]]
#> [1] "A2M"
#> 
#> [[3]]
#> [1] "A2MP1"
#> 
#> [[4]]
#> [1] "NAT1"
#> 
#> [[5]]
#> [1] "NAT2"
#> 
#> [[6]]
#> [1] "SERPINA3"
#>