Gene functional descriptions

Usage

description(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

DFrame.

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.

This file is malformed on the WormBase FTP server for WS270 and WS271 releases.

Updated 2023-09-25.

Examples

x <- description()
#> → Importing /Users/mike/.cache/R/WormBase/BiocFileCache/bb8f58a2ea31_c_elegans.PRJNA13758.WS289.functional_descriptions.txt.gz using base::`readLines()`.
print(x)
#> DataFrame with 52109 rows and 4 columns
#>                        geneId     conciseDescription   automatedDescription
#>                   <character>            <character>            <character>
#> WBGene00000001 WBGene00000001 aap-1 encodes the C... Enables protein kina..
#> WBGene00000002 WBGene00000002 aat-1 encodes an ami.. Contributes to L-ami..
#> WBGene00000003 WBGene00000003 aat-2 encodes a pred.. Predicted to enable ..
#> WBGene00000004 WBGene00000004 aat-3 encodes an ami.. Contributes to L-ami..
#> WBGene00000005 WBGene00000005 aat-4 encodes a pred.. Predicted to enable ..
#> ...                       ...                    ...                    ...
#> WBGene00306126 WBGene00306126                     NA Predicted to be invo..
#> WBGene00306131 WBGene00306131                     NA                     NA
#> WBGene00306132 WBGene00306132                     NA Is affected by sever..
#> WBGene00306133 WBGene00306133                     NA Is affected by sir-2..
#> WBGene00306134 WBGene00306134                     NA Is affected by sir-2..
#>                  geneClassDescription
#>                           <character>
#> WBGene00000001 phosphoinositide kin..
#> WBGene00000002 Amino Acid Transport..
#> WBGene00000003 Amino Acid Transport..
#> WBGene00000004 Amino Acid Transport..
#> WBGene00000005 Amino Acid Transport..
#> ...                               ...
#> WBGene00306126 CASP homolog of nema..
#> WBGene00306131             not known 
#> WBGene00306132             not known 
#> WBGene00306133 Alternative N-termin..
#> WBGene00306134 SXP /RAL-2-Like prot..