makeFastANIDistMatrix: Make a distance matrix from FastANI output (tab-delimited...

In wanyuac/handyR: Handy functions for R programming.

Make a distance matrix from FastANI output (tab-delimited file)

Description

This function coverts a FastANI output into a distance matrix.

Usage

makeFastANIDistMatrix(f, keep_asym = FALSE, frac = FALSE, suffix = "fasta")

Arguments

f	Path to the tab-delimited output file of FastANI
keep_asym	A logical flag specifying whether to keep the original asymmetric distance matrix.
frac	A logical flag specifying whether to convert percentages to decimal fractions. This option does not affect the tree topology as the change is proportional.
suffix	Filename extension of input FASTA files for FastANI, such as fna and fasta.

Value

One or two n-by-n distance matrices (depending on keep_asm), where n denotes the number of genomes.

Author(s)

Yu Wan ([e-mail])

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