restrictTaxLevel: Restrict microbe signatures to specific taxonomic levels

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

Restrict microbe signatures to specific taxonomic levels

Description

Functionality for restricting microbe signatures to specific taxonomic levels such as genus and species.

Usage

restrictTaxLevel(df, tax.level = "mixed", exact.tax.level = TRUE, min.size = 1)

Arguments

df	data.frame storing BugSigDB data. Typically obtained via importBugSigDB.
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 signatures. Use min.size = 0 to keep empty signatures.

Value

a data.frame with microbe signature columns restricted to chosen taxonomic level(s).

References

BugSigDB: https://bugsigdb.org

See Also

importBugSigDB

Examples

 df <- importBugSigDB()
 df <- restrictTaxLevel(df, tax.level = "genus")

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