Fetch all genes

Fetch identifiers for all genes.

fetchAllGenes(species, types = NULL, config = NULL)

Arguments

species

String specifying the taxonomy ID of the species of interest.

types

Character vector specifying the types of gene identifiers to return. If NULL, the available types are determined from fetchGeneTypes.

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 identifiers of the specified type for each gene.

Author

Aaron Lun

Examples

out <- fetchAllGenes("9606")
head(out)
#>   entrez      ensembl   symbol
#> 1      1 ENSG0000....     A1BG
#> 2      2 ENSG0000....      A2M
#> 3      9 ENSG0000....     NAT1
#> 4     10 ENSG0000....     NAT2
#> 5     12 ENSG0000.... SERPINA3
#> 6     13 ENSG0000....    AADAC
head(out$symbol)
#> [[1]]
#> [1] "A1BG"
#> 
#> [[2]]
#> [1] "A2M"
#> 
#> [[3]]
#> [1] "NAT1"
#> 
#> [[4]]
#> [1] "NAT2"
#> 
#> [[5]]
#> [1] "SERPINA3"
#> 
#> [[6]]
#> [1] "AADAC"
#>