Download and process conversion tables

Helper function to download and process tables converting UniProt IDs to PomBase/WormBase IDs. The PomBase-UniProt ID conversion table is downloaded from https://www.pombase.org/data/names_and_identifiers/PomBase2UniProt.tsv. The WormBase-UniProt ID conversion table is downloaded from https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/CAEEL_6239_idmapping.dat.gz.

getConvTable(type)

Arguments

type

Character scalar, either "PomBase" or "WormBase".

Value

A data.frame with ID conversion information.

Author

Charlotte Soneson

Examples

df <- getConvTable(type = "PomBase")
head(df)
#>      PomBaseID UniProtID
#> 1  SPAC1002.01    Q9US57
#> 2  SPAC1002.02    Q9US56
#> 3 SPAC1002.03c    Q9US55
#> 4 SPAC1002.04c    Q9US54
#> 5 SPAC1002.05c    Q9US53
#> 6 SPAC1002.06c    Q9US52

df <- getConvTable(type = "WormBase")
head(df)
#>   UniProtID UniProtKB.ID     WormBaseID
#> 1    P41932        14331 WBGene00003920
#> 2    Q20655        14332 WBGene00001502
#> 3    O18178         2A51 WBGene00012348
#> 4    Q09543         2AAA WBGene00003901
#> 5    G5EDR3         2AB1 WBGene00006352
#> 6    Q19341         3HAO WBGene00010595