outliers_dropped: Identifies original accession number of given haplotype index...

In EvolEcolGroup/mtDNAcombine: R package to download, combine, and curate sequences from public databases

Description

outliers_dropped

Usage

outliers_dropped(max_mutations, info_df)

Arguments

max_mutations	user defined value for number of mutations allowed before haplotype/sample considered an outlier
info_df	expected to be info_df or structured as info_df built from earlier functions. Either read in file or use object of correct format.

Details

Finds aligned sequence data for the populations with samples that are over a user defined value for maximum number of mutations on a branch before being considered to be an outlier. Haplotype networks are plotted and outlier sequences are dropped from fasta files.

Function identifies populations that have samples separated by a number of mutations greater than a user defined value for being considered an outlier. Outlier sequences are dropped from fasta files, haplotype networks replotted and new files written out with prefix 'new_'.

EvolEcolGroup/mtDNAcombine documentation built on July 8, 2021, 10:30 p.m.