combine_identicalmutations: Combine identical mutations

In SimRVSequences: Simulate Genetic Sequence Data for Pedigrees

Description

Assuming that all mutations are of the same type (in SLIM simulation), different mutations at the same site are actually identical mutations from different lineages. This function re-codes these mutations so that they are only cataloged once.

Usage

combine_identicalmutations(mutmap, hapmat, mut_type)

Arguments

mutmap	data.frame. The SNV_map with identical mutations
hapmat	sparseMatrix. The sparseMatrix of haplotypes
mut_type	character. the name of the mutation type for which to re-code identical mutations

Value

A list containing:

hapmat	A sparse matrix of haplotypes. See details.
mutmap	A data frame cataloging SNVs in hapmap.

SimRVSequences documentation built on July 1, 2020, 6:03 p.m.