Gene functional descriptions

description(version = NULL, progress = FALSE)

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").

progress

logical(1). Show progress using pbapply package.

Value

tbl_df.

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.

Examples

x <- description()
#> Transmitting files from ftp.wormbase.org.
#> Files matching pattern: #> c_elegans.PRJNA13758.WS269.functional_descriptions.txt.gz
#> Downloading c_elegans.PRJNA13758.WS269.functional_descriptions.txt.gz.
#> Parsing lines in file...
#> Processing functional descriptions...
glimpse(x)
#> Observations: 51,254 #> Variables: 5 #> $ geneID <chr> "WBGene00000001", "WBGene00000002", "WBGene000… #> $ conciseDescription <chr> "aap-1 encodes the C. elegans ortholog of the … #> $ provisionalDescription <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ automatedDescription <chr> "aap-1 is an ortholog of human PIK3R1 (phospho… #> $ geneClassDescription <chr> "phosphoinositide kinase AdAPter subunit", "Am…