cross: cross

In USDA-ARS-GBRU/crossword: Breeding program similation sotware

cross

Description

The function is used to create haplotype information based on the input
it uses "create_scheme_from_single_population" and "create_scheme" local function to create the scheme
and "create_parent" and "cross" functions of 'simcross' package
The function creates scheme from the provided parental information:
1. single parent1 X single parent2
2. single parent1 X list of parents2
3. list of parents1 X single parent2
combinations of list of parents1 X list of parents2 is not allowed

Usage

cross(P1,P2,N,id,chr_length,parental_genotypes,isdh)

Arguments

P1	Required: parent/s 1, a name or a list of names of the parents 1
P2	Optional: parent/s 2, a name or a list of names of the parents 2 If it is missing, the multiple cross will be applied for all parents listed in parent 1 which should be > two parents
N	Required: number of individuals in each repeated generation
id	Required: ID of the current breeding procedure
chr_length	Required: a two-column file of chromosomes' IDs and length in CM
parental_genotypes	Required: a parental_genotypes object
isdh	Optional: is double habloid ?

Value

The output is a structured object of: 1. scheme: contains the pedigree information of all haplotypes in a data frame of four columns:
1.haplotype IDs
2.generation
3.parent 1
4.parent 2
2. haplotype: contains the haplotype genetic architect for all haplotypes
each haplotype has sub datasets of chromosomes and each chromosome has the maternal (mat) and paternal (pat) information which is allele structure and loci

Examples

chr_length = "chr_len.txt"
parental_genotypes = get_parental_genotypes(input,gen2phy,homo)
pop1 = cross("grg","tg",400,'pop1',chr_length,parental_genotypes)

USDA-ARS-GBRU/crossword documentation built on May 23, 2024, 11:45 p.m.