Obtain published microbial signatures from bugsigdb.org

Source: R/bugsigdb.R

Obtain published microbial signatures from bugsigdb.org

importBugSigDB(version = "10.5281/zenodo.13997429", 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.

Value

a data.frame.

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.

Examples


 df <- importBugSigDB()
#> Using cached version from 2024-10-30 16:00:33