is_clade: Test if a lineage belongs to a clade

In yatah: Yet Another TAxonomy Handler

Test if a lineage belongs to a clade

Description

Test if a lineage belongs to a clade

Usage

is_clade(lineage, clade, rank = c(".", yatah::all_ranks))

Arguments

lineage	string. Vector of lineages.
clade	string.
rank	string. One of c("kingdom", "phylum", "class", "order", "family", "genus", "species", "strain") with partial matching.

Details

If rank is set to ., clade is looked for among all ranks.

Value

logical.

Examples

lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
is_clade(c(lineage1, lineage2), clade = "Verrucomicrobia", rank = "phylum")
is_clade(c(lineage1, lineage2), clade = "Clostridia")

yatah documentation built on May 29, 2024, 6:11 a.m.