sim.array: 'A progeny array simulator.'
In yangjl/imputeR: Imputation of GBS genotypes via window phasing

Description Usage Arguments Value Examples

Simulate a S4 GBS.array object with true_parents, gbs_parents, true_kids, gbs_kids and pedigree.

sim.array(size.array, numloci, hom.error = 0.02, het.error = 0.8,
  rec = 0.25, selfing = 0.5, imiss = 0.5, misscode = 3)

kid(p1, p2, het.error, hom.error, rec, imiss, misscode)

ran.hap(numloci, p)

add_error(diploid, hom.error, het.error)

copy.mom(mom, co_mean)

missing.idx(nloci, imiss)

`size.array`	Size of the progeny array.
`numloci`	Number of loci to simulate.
`hom.error`	Homozygous error rate, default=0.02.
`het.error`	Heterozygous error rate, default=0.8.
`rec`	Recombination rate, default=0.25.
`selfing`	Proportion of selfed progeny, default=0.5.
`imiss`	Individual missing rate, default=0.5.
`misscode`	Missing code, default=3.
`p1`	first parent (a list)
`p2`	second parent (a list)
`p`	a vector of allele freq with length numloci.
`diploid`	a vector of diploid genotype, for example, c(0, 1, 1, 0, 2, 2).
`mom`	a list of mom's haplotype.
`co_mean`	mean number of crossovers per chromosome.
`numloci`	number of loci.
`hom.error`	homozygous error rate.
`het.error`	heterozygous error rate.

Return GBS.array object.

Slot1: true_parents, a list of data.frame(hap1, hap2). Slot2: gbs_parents, a list of genotypes. For example, c(1, 2, 2, 0, 3). Slot3: true_kids, a list of data.frame(hap1, hap2). Slot4: gbs_kids, a list of kid genotypes. For example, c(1, 1, 3, 1, 2). Slot5: pedigree, a data.frame (kid, p1, p2). Note, p1 is the focal parent. Slot6: freq, a vector of reference allele freq for all SNPs.

See https://github.com/yangjl/imputeR/blob/master/vignettes/imputeR-vignette.pdf for more details.

a list of true [[1]] and observed [[2]] kid

a vector of genotype,

a vector of diploid genotype.

test <- sim.array(size.array=50, numloci=10)
class(test)

ran.hap(3, c(0.5, 0.8, 0.1))

add_error(c(0, 1, 1, 0, 2, 2), 0.02, 0.8)

copy.mom(list(c(0, 1, 1, 0, 1, 1)), 0.25)