Man pages for eriqande/gscramble
Simulating Admixed Genotypes Without Replacement
| check_chrom_lengths | check that the chromosome lengths are acceptable given... |
| check_gsp_for_validity_and_saturation | Check that GSP does not reuse genetic material and yet uses... |
| check_pedigree_for_inbreeding | Check the a GSP (in prepped list format) for inbreeding loops |
| check_rec_rates_formatting | check to make sure that the recombination rates tibble is... |
| check_reppop | check that the RepPop is formatted correctly |
| computeQs_from_segments | return the admixture fractions of sampled individuals |
| create_GSP | Create a GSP from user inputs about what type of hybrids from... |
| 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... |
| gsp4 | Tibble holding specification for a 7 member genomic... |
| GSP_opts | A list of tibbles specifying the pedigrees available from... |
| I_meta | Metadata for 78 individuals |
| make_subscript_matrix | makes a two-column matrix for subscripting alleles out of a... |
| 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... |
| plink2gscramble | read plink-formatted .map and .ped files into 'gscramble'... |
| plink_map2rec_rates | Convert a PLINK map file to 'gscramble' RecRates bins in a... |
| 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... |
| rearrange_genos | rearrange genotypes into separate columns for each haplotype. |
| recomb_point | Randomly sample the positions of recombinations on a... |
| 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... |
| seg_haps_through_gsp | Segregate haplotypes through a genome simulation pedigree... |
| segments2markers | Map alleles from scrambled founders to the sampled segments... |
| segregate | Segregate segments down genomic simulation pedigrees |
| sim_level_founder_haplos | computes the simulation-level founder haplotype index for... |
| tidy_up_sampled_haplos | takes the waka_waka table and returns a simple tibble with... |
| xover | internal function to do crossovers and create recombinations |
