combine_identicalmutations: Combine identical mutations

Description Usage Arguments Value

View source: R/SlimFunctions.R

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

1
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.