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

Source: R/eigenstrat.R

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