Other gene identifiers

geneOtherIDs(version = getOption(x = "wormbase.version", default = NULL))

Arguments

version

character(1) or NULL. WormBase version. If NULL (recommended), defaults to current production release version available on the WormBase website. Legacy versions can be specified as a character string (e.g. "WS262").

Value

DataFrame.

Note

As of WS269 release, some non-N2 gene IDs are included in the flat files available on the WormBase FTP server. These annotations are removed from the return here, using grep matching to return only WBGene entries.

Updated 2019-08-28.

Examples

## WormBase FTP server must be accessible. tryCatch( expr = geneOtherIDs(), error = function(e) e )
#> Transmitting files from <ftp.wormbase.org>.
#> Files matching pattern: c_elegans.PRJNA13758.WS277.geneOtherIDs.txt.gz
#> → Downloading c_elegans.PRJNA13758.WS277.geneOtherIDs.txt.gz.
#> → Importing c_elegans.PRJNA13758.WS277.geneOtherIDs.txt.gz at /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpRU0dkX using readr::`read_lines()`.
#> DataFrame with 52086 rows and 2 columns #> geneID geneOtherIDs #> <character> <list> #> 1 WBGene00000001 Y110A7A.10,aap-1 #> 2 WBGene00000002 F27C8.1,aat-1 #> 3 WBGene00000003 F07C3.7,aat-2 #> 4 WBGene00000004 F52H2.2,aat-3 #> 5 WBGene00000005 T13A10.10,aat-4 #> ... ... ... #> 52082 WBGene00306071 mha-1 #> 52083 WBGene00306072 mha-2 #> 52084 WBGene00306073 mha-3 #> 52085 WBGene00306076 Y53C10A.25 #> 52086 WBGene00306078 Y51H7C.42