get_all_clades: Extract all clades present in the lineages
In abichat/yatah: Yet Another TAxonomy Handler

get_all_clades

R Documentation

Extract all clades present in the lineages

Description

Extract all clades present in the lineages

Usage

get_all_clades(lineage, simplify = TRUE)

Arguments

`lineage`	string. Vector of lineages.
`simplify`	logical. Should the output be a vector or a dataframe?

Details

If a clade correspond to different ranks (e.g. Actinobacteria is both a phylum and a clade), it will be displayed only one time when simplify is set to TRUE. It is also the case for different clades with same name and same rank when simplify is set to FALSE.

Value

The clades present in the lineage. Vector of ordered strings or data.frame.

Examples

lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
lineage3 <- "k__Bacteria|p__Actinobacteria|c__Actinobacteria"
get_all_clades(c(lineage1, lineage2, lineage3))
get_all_clades(c(lineage1, lineage2, lineage3), simplify = FALSE)

abichat/yatah documentation built on April 14, 2024, 7:25 a.m.