R/feature_ignore_singletons.R

In statgenlmu/coala: A Framework for Coalescent Simulation

ign_singletons_class <- R6Class("ign_singletons", inherit = feature_class)


#' Feature: Ignore Singletons
#'
#' Mutations that are observed in just one haplotype ('singletons') are often
#' regarded as likely candidates for sequencing errors. Sometimes, it can be
#' advantageous to exclude them from an analysis. This feature removes all
#' singletons from the simulated data before the summary statistics are
#' calculated.
#'
#' This function assumes that a singleton is a mutation for which the derived
#' allele is observed exactly once in all sequences, regardless of the
#' population structure.
#'
#' @export
#' @template feature
#' @examples
#' model <- coal_model(2, 1) +
#'   feat_mutation(10) +
#'   feat_ignore_singletons() +
#'   sumstat_sfs("n_mut", transformation = sum)
#' # In this model, all mutations are singletons. Therefore,
#' # the number of mutations is 0 when removing singletons:
#' simulate(model)$n_mut
feat_ignore_singletons <- function(locus_group = "all") {
  ign_singletons_class$new(locus_group = locus_group)
}


has_ign_singletons <- function(model) {
  any(vapply(get_features(model), inherits,
             what = "ign_singletons", logical(1)))
}


remove_singletons <- function(segsites_list) {
  lapply(segsites_list, function(segsites) {
    is_singleton <- colSums(get_snps(segsites)) == 1
    segsites[, !is_singleton]
  })
}


#' @describeIn conv_to_ms_arg Feature conversion
#' @export
conv_to_ms_arg.ign_singletons <- ignore_par #nolint

#' @describeIn conv_to_ms_arg Feature conversion
#' @export
conv_to_msms_arg.ign_singletons <- ignore_par #nolint

#' @describeIn conv_to_ms_arg Feature conversion
#' @export
conv_to_scrm_arg.ign_singletons <- ignore_par #nolint

#' @describeIn conv_to_ms_arg Feature conversion
#' @export
conv_to_seqgen_arg.ign_singletons <- ignore_par #nolint