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

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"))

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 from a downstream analysis.

Examples

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: object 'snps' not found
results_d <- d(W = "French", X = "Dinka", Y = "Altai", Z = "Chimp", data = snps_tv)
#> Error: object 'snps_tv' not found
 # \dontrun{}