load_fasta {rhierbaps}

load_fasta

Description

Loads a fasta file into matrix format ready for running the hierBAPS algorithm.

Usage

load_fasta(msa, keep.singletons = FALSE)

Arguments

msa

Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered

keep.singletons

A logical indicating whether to consider singleton mutations in calculating the clusters

Value

A character matrix with filtered SNP data

Examples

msa <- system.file("extdata", "seqs.fa", package = "rhierbaps")
snp.matrix <- load_fasta(msa)