Peptides

peptides(
  version = getOption(x = "wormbase.version", default = NULL),
  BPPARAM = BiocParallel::bpparam()
)

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").

BPPARAM

bpparamClass. BiocParallel parameter to specify the desired processor configuration.
We recommend using one of the following:

Value

SplitDataFrameList. Split by geneID column.

Note

Updated 2020-01-26.

Examples

## WormBase FTP server must be accessible. tryCatch( expr = peptides(), error = function(e) e )
#> Transmitting files from <ftp.wormbase.org>.
#> Files matching pattern: c_elegans.PRJNA13758.WS277.wormpep_package.tar.gz
#> → Downloading c_elegans.PRJNA13758.WS277.wormpep_package.tar.gz.
#> → Importing wormpep.table277 at /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpRU0dkX using readr::`read_lines()`.
#> → Processing peptides.
#> SplitDataFrameList of length 19998 #> $WBGene00007063 #> DataFrame with 2 rows and 8 columns #> geneID wormpep status uniprot insdc sequence locus #> <factor> <factor> <factor> <factor> <factor> <factor> <factor> #> 1 WBGene00007063 CE32090 Confirmed A4F336 CCD61130.1 2L52.1a NA #> 2 WBGene00007063 CE50569 Confirmed A0A0K3AWR5 CTQ86426.1 2L52.1b NA #> product #> <factor> #> 1 NA #> 2 NA #> #> $WBGene00007064 #> DataFrame with 3 rows and 8 columns #> geneID wormpep status uniprot insdc sequence locus #> <factor> <factor> <factor> <factor> <factor> <factor> <factor> #> 1 WBGene00007064 CE32785 Confirmed A4F337 CCD61138.1 2RSSE.1a rga-9 #> 2 WBGene00007064 CE48524 Confirmed U4PAK0 CDH92922.1 2RSSE.1b rga-9 #> 3 WBGene00007064 CE52653 Confirmed A0A2X0T1Z3 SPS41576.1 2RSSE.1c rga-9 #> product #> <factor> #> 1 Rho-GAP domain-containing protein #> 2 Rho-GAP domain-containing protein #> 3 Rho-GAP domain-containing protein #> #> $WBGene00007065 #> DataFrame with 2 rows and 8 columns #> geneID wormpep status uniprot insdc sequence locus #> <factor> <factor> <factor> <factor> <factor> <factor> <factor> #> 1 WBGene00007065 CE24758 Confirmed G5EFG7 CAA21777.2 3R5.1a pot-3 #> 2 WBGene00007065 CE47782 Confirmed J7SA53 CCM09397.1 3R5.1b pot-3 #> product #> <factor> #> 1 POT1PC domain-containing protein #> 2 POT1PC domain-containing protein #> #> ... #> <19995 more elements>