Simulating Admixed Genotypes Without Replacement

---

Documentation for package ‘gscramble’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

check_chrom_lengths	check that the chromosome lengths are acceptable given recombination rates
check_gsp_for_validity_and_saturation	Check that GSP does not reuse genetic material and yet uses all of it
check_pedigree_for_inbreeding	Check the a GSP (in prepped list format) for inbreeding loops
computeQs_from_segments	return the admixture fractions of sampled individuals
create_GSP	Create a GSP from user inputs about what type of hybrids from which populations to create hybrids
drop_segs_down_gsp	High level function for dropping segments down a GSP
example_chrom_lengths	Lengths of the three chromosomes used in the example data set
example_segments	Example of a segments tibble
Geno	Genotype matrix of 78 individuals and 100 SNP markers
gscramble2newhybrids	Convert 'gscramble' output to newhybrids format
gscramble2plink	Write 'gscramble' I_meta, M_meta, and Geno to a plink file
GSP	Example Genomic Simulation Pedigree, GSP, with 13 members
gsp2dot	Write a dot file to represent a genome simulation pedigree
gsp3	Tibble holding specification for a 5 member genomic permutation pedigree.
gsp4	Tibble holding specification for a 7 member genomic permutation pedigree.
GSP_opts	A list of tibbles specifying the pedigrees available from 'createGSP()'
I_meta	Metadata for 78 individuals
mat_scramble	Scramble a matrix of genotype data
M_meta	Metadata for 100 molecular markers
perm_gs_by_pops	Take the output of rearrange_genos and permute everyone by population
plink2gscramble	read plink-formatted .map and .ped files into 'gscramble' format
plink_map2rec_rates	Convert a PLINK map file to 'gscramble' RecRates bins in a tibble
plot_simulated_chromomsome_segments	Plot the simulated chromosomes of an individual
prep_gsp_for_hap_dropping	Take a gsp in tibble form and make a list suitable for gene dropping
rearrange_genos	rearrange genotypes into separate columns for each haplotype.
recomb_point	Randomly sample the positions of recombinations on a chromosome
RecRates	Recombination rate data for many roughly 1 Mb bins
renumber_GSP	Renumber GSP members by adding a constant to each
RepPop1	A simple example of a reppop table
RepPop4	Another simple example of a reppop table
seg2tib	Takes a gamete in segment format and returns a tibble with Pop and indiv_index
segments2markers	Map alleles from scrambled founders to the sampled segments from a GSP.
segregate	Segregate segments down genomic simulation pedigrees
sim_level_founder_haplos	computes the simulation-level founder haplotype index for each founder haplo
xover	internal function to do crossovers and create recombinations