sim_filter_generated_data: This function filters the generated gamete data so that the...

In mccoy-lab/rhapsodi: R haploid sperm/oocyte data imputation

This function filters the generated gamete data so that the sparse input data only reflects heterozygous SNPs

Description

This function is used to filter the generated data such that the sparse gamete data only reflects heterozygous SNPs (one 0 and one 1) Then we only keep these SNP indices for the full gamete data and the diploid donor haplotypes Further, if de novo mutations were simulated, we filter the list of DNM locations to reflect those that weren't filtered out. However, we don't return the filtered dnm list, we just output it as a message

Usage

sim_filter_generated_data(
  gam_na_df,
  gam_full_df,
  donor_haps,
  new_rows,
  add_de_novo_mut
)

Arguments

gam_na_df	the generated, sparsified gamete data with SNP indices in the first column
gam_full_df	the generated full gamete data with SNP indices in the first column
donor_haps	the generated diploid donor phased haplotypes
new_rows	a vector of the integer SNP indices for where de novo mutation were added if DNMs were simulated, this should be NULL otherwise
add_de_novo_mut	a bool, if TRUE de novo mutations were simulated in the generative model and then new_rows is also filtered

Value

out a named list with the filtered gam_na_df, filtered gam_full_df, filtered donor_haps, new number of snps after filtering num_snps

mccoy-lab/rhapsodi documentation built on July 27, 2022, 3:56 a.m.