extractTaxLevel: Extract specific taxonomic levels from a microbe signature

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

Extract specific taxonomic levels from a microbe signature

Description

Functionality for extracting specific taxonomic levels (such as genus and species) from a microbe signature containing taxonomic clades in MetaPhlAn format.

Usage

extractTaxLevel(
  sig,
  tax.id.type = c("metaphlan", "taxname"),
  tax.level = "mixed",
  exact.tax.level = TRUE
)

Arguments

sig	character. Microbe signature containing taxonomic clades in MetaPhlAn format.
tax.id.type	Character. Taxonomic ID type of the returned microbe sets. Either "metaphlan" (default) 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.

Value

a character vector storing taxonomic clades restricted to chosen taxonomic level(s).

References

BugSigDB: https://bugsigdb.org

Examples

 ord <- "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales"
 sig <- c("f__Lactobacillaceae|g__Lactobacillus",
          "f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva",
          "f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae")
 sig <- paste(ord, sig, sep = "|")
 sig <- extractTaxLevel(sig, tax.level = "genus")
 sig <- extractTaxLevel(sig, tax.level = "genus", exact.tax.level = FALSE)
 sig <- extractTaxLevel(sig,
                        tax.id.type = "taxname",
                        tax.level = "genus",
                        exact.tax.level = FALSE)

waldronlab/bugsigdbr documentation built on May 2, 2024, 1:21 p.m.