taxtable: Convert results from different taxonomic assignment...

In brendanf/phylotax: Refine taxonomic assignment of environmental sequences using a taxonomic tree

Description

Convert results from different taxonomic assignment algorithms to a uniform format

Usage

taxtable(tax, ...)

taxtable_sintax(tax, min_confidence = 0, ...)

taxtable_idtaxa(tax, min_confidence = 0, seq_id = NULL, ...)

taxtable_dada2(tax, min_confidence = 0, ...)

Arguments

tax	Results from taxonomy()
...	passed to methods
min_confidence	(integer) The minimum confidence to include in results. May be higher than the value given in taxonomy(), but will have no effect if it is lower.
seq_id	(character vector) names for the sequences; these will be the values that end up in the "label" column. If not given explicitly, they are taken from the taxonomy results if this is possible.

Value

a tibble::tibble() with columns:

label

sequence identifier

rank

the rank of the assignment

taxon

the taxon which was assigned

confidence

the confidence of the assignment

Each query sequence will typically occupy several rows of the output, one for each rank which was assigned.

brendanf/phylotax documentation built on March 3, 2021, 2:21 p.m.