is_clade {yatah}

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")