gene_distance: Compute gene similarity (or distance) for gene profiles

In tvatanen/microbiomics: Microbiomics

Description

This functions returns gene similarity / distance based on microbial gene profiles given as input. Gene similarity between two clades / genomes is the number of common genes between the genomes divided by the number of genes in the smaller genome, as defined in https://www.ncbi.nlm.nih.gov/pubmed/9916801 Gene distance is '1 - gene similarity'. #'

Usage

gene_distance(x, return_similarity = FALSE)

Arguments

x	data frame or matrix (genomes x genes) containing gene profiles
return_similarity	set TRUE to return similarity instead of distance

Value

a dist object containing gene similarities / distances

Author(s)

Tommi Vatanen <[e-mail]>

tvatanen/microbiomics documentation built on Sept. 27, 2019, 7:29 a.m.