AILped |
Example AIL pedigree |
calc_Lstar |
Calculate adjusted chromosome length for obligate chiasma |
CCcolors |
Collaborative Cross colors |
check_pedigree |
Check a pedigree for errors |
collapse_do_alleles |
Collapse alleles for simulated DO genotypes |
convert2geno |
Convert continuous allele information into marker genotypes |
convert2geno_allchr |
Convert continuous allele information into marker genotypes for multiple chromosomes |
create_parent |
Create a parent object |
cross |
Cross two individuals |
get_geno |
Get genotype at a single position |
mouseL_cox |
Mouse chromosome lengths |
mouseL_mgi |
Mouse chromosome lengths |
plot_crosslines |
Plot cross lines |
plot_ind |
Plot an individual |
sim_4way_pedigree |
Simulate pedigree for 4-way intercross |
sim_ail_pedigree |
Simulate AIL pedigree |
sim_ail_pedigree_fix_n |
Simulate AIL pedigree with fixed n |
sim_crossovers |
Simulate crossover locations using the Stahl model |
sim_dof1_pedigree |
Simulate pedigree for F1 between diversity outbreds and another inbred line |
sim_do_pedigree |
Simulate a pedigree for Diversity Outbred mice |
sim_do_pedigree_fix_n |
Simulate a pedigree for Diversity Outbreds for a target sample size |
sim_from_pedigree |
Simulate genotypes for pedigree |
sim_from_pedigree_allchr |
Simulate genotypes for pedigree for multiple chromosomes |
sim_meiosis |
Simulate meiosis |
sim_ril_pedigree |
Generate a ril pedigree |
where_het |
Find heterozygous regions |