trim_rank: Trim lineages until a specified rank
In abichat/yatah: Yet Another TAxonomy Handler

trim_rank

R Documentation

Trim lineages until a specified rank

Description

Trim lineages until a specified rank

Usage

trim_rank(lineage, rank = yatah::all_ranks, same = TRUE)

Arguments

`lineage`	string. Vector of lineages.
`rank`	string. One of `c("kingdom", "phylum", "class", "order", "family", "genus", "species", "strain")` with partial matching.
`same`	logical. Does the lineage have the same depth? Default to `TRUE`.

Details

Returns NA if a lineage is not as deep as the specified rank.

Value

The trimmed lineages. Depth could be different among them.

Examples

lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
trim_rank(c(lineage1, lineage2), rank = "phylum")
trim_rank(c(lineage1, lineage2), rank = "genus")

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