designcode

The second required input for RABBIT is pedinfo, providing the pedigree information of a mapping population in form of pedfile or designcode.

For a non-subdivided population, pedinfo can often be provided by a string designcode. There are three kinds of designcode: commcross, breedcross, and juncdist. If pedinfo is provided by a designcode in form of commoncross or juncdist, samples in the genofile must be ordered such that founders always precede offspring. All samples in genofile are offspring, except the founders that are implied by designcode.

See MagicBase.parsedesign for parsing designcode into a struct. See MagicBase.vcf_extract_pedfile for extracting pedfile from a vcf genofile and a given designcode of the non-subdivided population.

commoncross

commoncross
  • "nril-selfm" where "nril" denotes n-way recombination inbred lines (RILs), and "selfm" denotes m generations of inbreeding by selfing, e.g. 8ril-self4. Founders are assumed to be exchangeable when parsing the designcode.
  • "nril-sibm" where "nril" denotes n-way RIL, and "sibm" denotes m generations of inbreeding by sibling, e.g. 8ril-sib20. Founders are assumed to be exchangeable when parsing the designcode.
  • "bcg-selfm" where "bcg" denotes g generations of back cross with the first parent, and "selfm" denotes m generations of inbreeding by selfing, e.g. bc2-self6. "bcg" is the same as "bcg-self0", e.g. "bc2".
  • "nstar-selfm" where "nstar" denotes star-like crosses between the first parent and each of the other parents, and "selfm" denotes m generations of inbreeding by selfing, e.g. 11star-self6. Note that "nstar-selfm" can be used in data simulation magicsimulate, but not in data analysis such as magicimpute. 
using MagicBase, Pedigrees
designinfo = parsedesign("4ril-self3";popid="4RIL")
plotped(designinfo.pedigree)
Example block output
designinfo = parsedesign("bc2-self3"; popid="BC")
plotped(designinfo.pedigree)
Example block output
designinfo = parsedesign("5star-self4"; popid="star")
plotped(designinfo.pedigree)
Example block output

breedcross

breedcross
  • designcode for breedcross is specified in form of pedcode=>nself, where pedcode specifies the multi-way cross and nself specifies the number of selfing generations following the multi-way cross.
  • Each cross is specified by "mother/g/father", where g is the generation of the offspring that is given by 1 + maximum of their parents' generations and the generation of a founder is set to 0. pedcode can be obtained by recursively specifying the pedcode of its parents. The notation "/g/" can be simplified to "/" for g=1 and to "//" for g=2.
  • nself must be a nonnegative integer, DH denoting double haploid, or FIXED denoting many generations of selfings. The DH is defined by internally setting nself=1 and ishomozygous = true for all offspring.
designinfo = parsedesign("P1/P2=>DH"; popid="DH")
plotped(designinfo.pedigree)
Example block output
designinfo = parsedesign("P1/4/P1/P2//P3/P4/3/P1/P2//P3/P4=>2"; popid="breedcross")
plotped(designinfo.pedigree)
Example block output

juncdist

juncdist
  • juncdist can be used to specify a mapping population without a known pedigree, for example, because of random mating in intermediate generations, if the average junction density such as map expansion can be estimated analytically or by simulation for given mate schemes.
  • juncdist assumes that the founders in each subpopulation are exchangeable. Internally isfglexch=true is set in offspringinfo for the offspring in the subpopulation.

The following shows an example designcode in form of juncdist.

designinfo = parsedesign("nfounder=3||ibd=1.0||mapexpansion=5.0")
designinfo.juncdist
JuncDist(3, 1.0, 5.0, nothing, nothing, nothing, nothing, nothing)

See MagicPrior.magicorigin for calculating junction densities from a pedigree.