Download Pathway Archive

Source: R/downloadPathwayArchive.R

Access the monthly archives of pathway content from WikiPathways.

downloadPathwayArchive(
  date = "current",
  organism = NULL,
  format = c("gpml", "gmt", "svg"),
  destpath = "./"
)

Arguments

date

(optional) The timestamp for a monthly release (e.g., 20171010) or "current" (default) for latest release.
organism

(optional) A particular species. See listOrganisms.
format

(optional) Either gpml (default), gmt or svg.
destpath

(optional) Destination path for file to be downloaded to. Default is current workding directory.

Value

Filename of downloaded file or an opened tab in default browser

Details

If you do not specify an organism, then an archive file will not be downloaded. Rather, the archive will be opened in a tab in your default browser.

See also

readPathwayGMT

Examples

# \donttest{
downloadPathwayArchive()  ## open in browser
downloadPathwayArchive(format="gmt")  ## open in browser
downloadPathwayArchive(date="20171010", format="svg")  ## open in browser
downloadPathwayArchive(date="20171010", organism="Mus musculus", format="svg")  ## download file

#> [1] "wikipathways-20171010-svg-Mus_musculus.zip"
downloadPathwayArchive(organism="Mus musculus")  ## download file

#> [1] "wikipathways-20210110-gpml-Mus_musculus.zip"
# }