Remove substitutions that are more likely to be a result of ancient DNA damage (C->T and G->A substitutions).
transversions_only(data, outfile = tempfile(fileext = ".snp"))
EIGENSTRAT data object.
Path to an output snp file with coordinates of excluded sites.
Updated S3 EIGENSTRAT data object with an additional 'exclude' slot specifying the path to the set of SNPs to be removed from a downstream analysis.
if (FALSE) # download an example genomic data set and prepare it for analysis
snps <- eigenstrat(download_data(dirname = tempdir()))
# perform the calculation only on transversions
snps_tv <- transversions_only(snps)
#> Error in eval(expr, envir, enclos): object 'snps' not found
results_d <- d(W = "French", X = "Dinka", Y = "Altai", Z = "Chimp", data = snps_tv)
#> Error in eval(expr, envir, enclos): object 'snps_tv' not found