lgeistlinger
commented
1 year ago This is how ?importBugSigDB looks now:
Obtain published microbial signatures from bugsigdb.org
Description:
Obtain published microbial signatures from bugsigdb.org
Usage:
importBugSigDB(version = "10.5281/zenodo.6468009", cache = TRUE)
Arguments:
version: character. A Zenodo DOI, git commit hash, or "devel".
Defaults to the most recent stable release on Zenodo, which
includes complete and reviewed content from BugSigDB. See
details.
cache: logical. Should a locally cached version used if available?
Defaults to ‘TRUE’.
Details:
There are three different options to obtain data from BugSigDB, as
determined by the ‘version’ argument.
• a Zenodo DOI: use this option if you would like to obtain one
of the stable release versions of BugSigDB on Zenodo. These
stable release versions of BugSigDB have been automatically
checked and manually reviewed and provide for the highest
data quality. Select this option if you would like to
incorporate BugSigDB into analysis and published research. If
not specified otherwise, the ‘importBugSigDB’ function will
obtain the most recent stable release from Zenodo by default.
• ‘"devel"’: use this option to obtain the latest version
("bleeding edge") of BugSigDB from the BugSigDBExports GitHub
repo (see references). Note that this will also include
incomplete and not reviewed content, which should be filtered
out prior to an analysis. Select this option if you are a
curator that actively contributes to BugSigDB and would like
to access data that you and other curators have recently
contributed to BugSigDB and that has not been included in a
stable release yet.
• a git commit hash: it might be occasionally of interest to
obtain a specific snapshot of the BugSigDBExports GitHub
repo, e.g. for the sake of debugging and troubleshooting.
This can be done by providing the short 7-character git
commit hash (SHA) or the full SHA of the export of choice. To
provide the full SHA, go to the BugSigDBExports commits page
(see references) and use the copy symbol to the left of the
7-character codes to copy the full SHA code of the export
version you want to use.
Value:
a ‘data.frame’.
References:
BugSigDB: <https://bugsigdb.org>
Stable release: <https://doi.org/10.5281/zenodo.5606165>
Latest version (incl. not reviewed content):
<https://github.com/waldronlab/BugSigDBExports>
BugSigDBExports commits page:
<https://github.com/waldronlab/BugSigDBExports/commits/main>I also updated the README of BugSigDBExports with a section what BugSigDBExports actually does, as there seem to have been some confusion as well.
@lwaldron Let me know whether this looks good, or whether this should be further enhanced. Please close the issue if this resolves the issue.
From https://github.com/waldronlab/BugSigDBExports/issues/19
@lgeistlinger I think the bugsigdbr vignette and import function should make clearer what the "devel" version does (and maybe even a message when using this option), because every active user is asking when changes to the wiki will be accessible from R.