sim_gameteFormation: Simulate formation of gametes.
In SimRVSequences: Simulate Genetic Sequence Data for Pedigrees

Simulate formation of gametes. This function will likely become an internal function.

1 2	sim_gameteFormation(chrom_map, allele_IDs, burn_in = 1000, gamma_params = c(2.63, 2.63/0.5))

`chrom_map`	Data.frame. A data.frame consisting of three columns: column 1 contains the chromosome numbers, column 2 start postion of chromosome (in cM), column 3 end position of chromosome (in cM).
`allele_IDs`	List of length 2. The identification numbers for the respective paternal and maternal alleles of the individual for whom we wish to simulate recombination. (Can accomodate numeric or string entries)
`burn_in`	Numeric. The "burn-in" distance in centiMorgan, as defined by Voorrips and Maliepaard (2012), which is required before simulating the location of the first chiasmata with interference. By default, `burn_in = 1000`. The burn in distance in cM. By default, `burn_in = 1000`.
`gamma_params`	Numeric list of length 2. The respective shape and rate parameters of the gamma distribution used to simulate distance between chiasmata. By default, `gamma` `_params` `= c(2.63, 2*2.63)`, as discussed in Voorrips and Maliepaard (2012).

A list containing the following:

chrom_haps A list of dataframes, each dataframe is a set of four recombined haplotypes for a single chromosome (in the order specified in chrom_map), each with a gamete group identifier column.

gamete_group A list of lists, each list contains the crossover positions for a single chromosome (in the order specified in chrom_map).

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