getSignatures: Obtain microbe signatures from BugSigDB

In waldronlab/bugsigdbr: R-side access to published microbial signatures from BugSigDB

Obtain microbe signatures from BugSigDB

Description

Functionality for obtaining microbe signatures from BugSigDB

Usage

getSignatures(
  df,
  tax.id.type = c("ncbi", "metaphlan", "taxname"),
  tax.level = "mixed",
  exact.tax.level = TRUE,
  min.size = 1
)

Arguments

df	data.frame storing BugSigDB data. Typically obtained via importBugSigDB.
tax.id.type	Character. Taxonomic ID type of the returned microbe sets. Either "ncbi" (default), "metaphlan", or "taxname".
tax.level	character. Either "mixed" or any subset of c("kingdom", "phylum", "class", "order", "family", "genus", "species", "strain"). This full vector is equivalent to "mixed".
exact.tax.level	logical. Should only the exact taxonomic level specified by tax.level be returned? Defaults to TRUE. If FALSE, a more general tax.level is extracted for microbes given at a more specific taxonomic level.
min.size	integer. Minimum signature size. Defaults to 1, which will filter out empty signature. Use min.size = 0 to keep empty signatures.

Value

a list of microbe signatures. Each signature is a character vector of taxonomic IDs depending on the chosen tax.id.type.

References

BugSigDB: https://bugsigdb.org

See Also

importBugSigDB

Examples

 df <- importBugSigDB()
 sigs <- getSignatures(df)

waldronlab/bugsigdbr documentation built on Oct. 31, 2024, 3:43 a.m.