sim_gameteInheritance: Simulate inheritance of parental gamete to offspring
In SimRVSequences: Simulate Genetic Sequence Data for Pedigrees

Description Usage Arguments Details Value

Simulate inheritance of parental gamete to offspring based on rare variant statuses of parent and offspring.

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sim_gameteInheritance(RV_locus, parent_RValleles, offspring_RVstatus,
  chrom_map, allele_IDs, burn_in = 1000, gamma_params = c(2.63,
  2.63/0.5))

`RV_locus`	Numeric list of length 2. A list containing (1) the chromosome upon which the rare variant resides (2) the position in cM where the rare variant resides.
`parent_RValleles`	Numeric list of length 2. The paternal and maternal alleles at the disease locus (1 = RV inherited, 0 otherwise)
`offspring_RVstatus`	Numeric. 1 if offspring inherits the RV from parent, 0 otherwise.
`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).

Here we use the RV statuses of the parent and offspring to determine which of the parental gametes are appropriate options for transmission. Upon reducing the sample space appropriately we choose from the remaining options with equal probability.

If the parent is not a carrier of the rare variant then we choose any of the four gametes with equal probability since the offpring could not have inherited the rare variant from this parent.
If the parent is a carrier of the rare variant and
- the offspring is not a carrier of the rare variant, we choose with equal probability from the two gametes that do not contain the rare variant.
- the offspring is a carrier of the rare variant, we choose with equal probability from the two gametes that docontain the rare variant.