High level function for dropping segments down a GSP — drop_segs_down

This one asks for the number of reps to do, and it also automatically does it over chromosomes and returns the results in a nice tidy tibble.

drop_segs_down_gsp(GSP, RR, Reps)

Arguments

GSP: the pedigree to use for the simulation, in the format of the package data GSP.
RR: the recombination rates in the format of the package data RecRates
Reps: the number of times to do the simulation. Different replicates are denoted by the index column in the output tibble.

Value

The output from this function is a tibble. Each row represents one segment of genetic material amongst the sampled individuals from the genomic permutation pedigrees. The columns give information about the provenance and destination of that segment as follows. Each segment exists in one of the samples (samp_index) from a sampled individual with a ped_sample_id

in a given samp_index within the individual. Further, it is on one of two gametes (gamete_index) that segregated into the individual, and it came from a certain founding population (pop_origin). And, of course, the segment occupies the space from start to end on a chromosome chrom. Finally, the index of the founder haplotype on the given gpp that this segement descended from is given in rs_founder_haplotype which is short for "rep-specific founder haplotype". This final piece of information is crucial for segregating variation from the individuals in the Geno file onto these segments. The gamete_segments column is a list column with duplicated entries for each chromosome in an individual.

Examples

simSegs <- drop_segs_down_gsp(GSP, RecRates, 4)