countPanGenes: Counting genes in a pangenome when randomly sampling a series...

In wanyuac/handyR: Handy functions for R programming.

Counting genes in a pangenome when randomly sampling a series of genomes

Description

This function is useful for creating gene-accumulation curves, also known as rarefaction curves.

Usage

countPanGenes(P, core = 0.95, hard_core = 0.99, permutations = 20)

Arguments

P	A binary presence-absence matrix with the dimension of n(genes) x n(isolates)
core	Threshold defining hard/soft-core genes (Default: >=0.95)
hard_core	Threshold defining hard-core genes (Default: >=0.99)
permutations	Number of sampling for each sample size (Default: 20; minumum: 3)

Value

A list of two lists ("num" and "avg"): one for gene counts and the other for mean gene counts.

Author(s)

Yu Wan ([e-mail])

wanyuac/handyR documentation built on June 10, 2024, 1:24 a.m.