find_revenants: Find genes that with matches that skip strata

In arendsee/phylostratr: Analyze phylostratigraphic data

Find genes that with matches that skip strata

Description

Find genes that with matches that skip strata

Usage

find_revenants(d, classifier = classify_by_evalue(1e-05))

Arguments

d	data.frame of maximal hits
classifier	function of a blast result that infers whether each subject species contains a homolog

Value

data.frame with columns [qseqid, ps, mrca, basal_ps, n]. Where qseqid is the focal species taxond IDs, ps is the phylostratum level (where 1 is generally cellular_organisms) of strata that are skipped, mrca is the taxon ID of the ancestor, basal_ps is the oldest stratum with a match to qseqid, and n is the total number of revenants for seqid.

arendsee/phylostratr documentation built on Dec. 31, 2022, 10:22 a.m.