recombine_gen: Recombines sequences in a generation

In philliplab/yasss: Yet Another Short Sequence Simulator

Description

Loops over the sequences in a generation, this function executes the following steps:

• Determine if the current sequence should undergo recombination

• Select the sequence that will be the recombinant partner

• Call recombine_seqs to recombine the sequences, and

• Populate the genealogy data.frame with all the recombination information.

Usage

recombine_gen(gen, ps_rate = 0)

Arguments

gen	A data.frame from a genealogy that contains just one generation
ps_rate	The chance that any given sequence will be a recombinant.

Details

The selection of the recombination partner is a random draw from all non-recombinant sequences in the generation. This is to prevent a sequences from effective under going two recombination events in a single cycle.

Value

A genealogy data.frame with the recombinants and the recombination related columns populated for each recombinant sequence.

philliplab/yasss documentation built on Sept. 7, 2020, 3:28 p.m.