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.
Value
The trimmed lineages. Depth could be different among them.
Details
Returns NA if a lineage is not as deep as the specified rank.
Examples
lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
trim_rank(c(lineage1, lineage2), rank = "phylum")
#> [1] "k__Bacteria|p__Verrucomicrobia" "k__Bacteria|p__Firmicutes"
trim_rank(c(lineage1, lineage2), rank = "genus")
#> [1] NA NA
