Gene identifiers

Usage

geneIds(release = getOption(x = "wormbase.release", default = NULL))

Arguments

release: character(1) or NULL. WormBase release. If NULL (recommended), defaults to current production release release available on the WormBase website. Legacy releases can be specified as a character string (e.g. "WS267").

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 2021-02-18.

Examples

x <- geneIds()
#> → Importing /Users/mike/.cache/R/WormBase/BiocFileCache/c22aa1bbbd9_c_elegans.PRJNA13758.WS289.geneIDs.txt.gz using base::`read.table()`.
print(x)
#> DataFrame with 52109 rows and 4 columns
#>                        geneId    geneName    sequence      status
#>                   <character> <character> <character> <character>
#> WBGene00000001 WBGene00000001       aap-1  Y110A7A.10        Live
#> WBGene00000002 WBGene00000002       aat-1     F27C8.1        Live
#> WBGene00000003 WBGene00000003       aat-2     F07C3.7        Live
#> WBGene00000004 WBGene00000004       aat-3     F52H2.2        Live
#> WBGene00000005 WBGene00000005       aat-4   T13A10.10        Live
#> ...                       ...         ...         ...         ...
#> WBGene00306126 WBGene00306126      cone-1 Y54F10AM.16        Live
#> WBGene00306131 WBGene00306131          NA   Y34B4A.20        Live
#> WBGene00306132 WBGene00306132          NA   F54D10.10        Live
#> WBGene00306133 WBGene00306133      azyx-1    F42G4.11        Live
#> WBGene00306134 WBGene00306134      srlf-8     F11F1.9        Live