# Simulating Admixed Genotypes Without Replacement

## Documentation for package ‘gscramble’ version 1.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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