Obtain microbe signatures from BugSigDB

Functionality for obtaining microbe signatures from BugSigDB

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.

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

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