keep_transitions {admixr}

Remove transversions (C->T and G->A substitutions)

Description

Remove substitutions that are more likely to be a result of ancient DNA damage (C->T and G->A substitutions).

Usage

keep_transitions(data, outfile = tempfile(fileext = ".snp"))

Arguments

data

EIGENSTRAT data object.

outfile

Path to an output snp file with coordinates of excluded sites.

Value

Updated S3 EIGENSTRAT data object with an additional 'exclude' slot specifying the path to the set of SNPs to be removed.