Orthologs

orthologs(
  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

DataFrame.

Note

Updated 2020-01-26.

Examples

## WormBase FTP server must be accessible. tryCatch( expr = orthologs(), error = function(e) e )
#> Transmitting files from <ftp.wormbase.org>.
#> Files matching pattern: c_elegans.PRJNA13758.WS277.orthologs.txt.gz
#> → Downloading c_elegans.PRJNA13758.WS277.orthologs.txt.gz.
#> → Importing c_elegans.PRJNA13758.WS277.orthologs.txt.gz at /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpRU0dkX using readr::`read_lines()`.
#> → Processing orthologs.
#> DataFrame with 20121 rows and 5 columns #> geneID #> <character> #> 1 WBGene00000001 #> 2 WBGene00000002 #> 3 WBGene00000003 #> 4 WBGene00000004 #> 5 WBGene00000005 #> ... ... #> 20117 WBGene00306003 #> 20118 WBGene00306004 #> 20119 WBGene00306005 #> 20120 WBGene00306013 #> 20121 WBGene00306076 #> danioRerio #> <list> #> 1 ENSDARG00000018060,ENSDARG00000034409,ENSDARG00000038524,... #> 2 ENSDARG00000005894,ENSDARG00000008100,ENSDARG00000020278,... #> 3 ENSDARG00000005894,ENSDARG00000008100,ENSDARG00000020278,... #> 4 ENSDARG00000005894,ENSDARG00000008100,ENSDARG00000010816,... #> 5 ENSDARG00000005894,ENSDARG00000008100,ENSDARG00000010816,... #> ... ... #> 20117 #> 20118 #> 20119 #> 20120 #> 20121 #> drosophilaMelanogaster homoSapiens #> <list> <list> #> 1 FBgn0020622 ENSG00000268173,ENSG00000278139 #> 2 FBgn0039844 #> 3 FBgn0002778,FBgn0028425,FBgn0039487 #> 4 FBgn0031064,FBgn0032911,FBgn0036493,... #> 5 FBgn0028425,FBgn0030574,FBgn0031064,... #> ... ... ... #> 20117 #> 20118 #> 20119 #> 20120 #> 20121 #> musMusculus #> <list> #> 1 ENSMUSG00000028698,ENSMUSG00000031834,ENSMUSG00000041417,... #> 2 ENSMUSG00000000958,ENSMUSG00000020600,ENSMUSG00000022180,... #> 3 ENSMUSG00000000958,ENSMUSG00000020600,ENSMUSG00000022180,... #> 4 ENSMUSG00000000958,ENSMUSG00000020600,ENSMUSG00000022180,... #> 5 ENSMUSG00000000958,ENSMUSG00000020600,ENSMUSG00000022180,... #> ... ... #> 20117 #> 20118 #> 20119 #> 20120 #> 20121