pedigreeHapCheck: check the consistency of haploblock genotypes over a pedigree

In PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

For all haploblocks, check whether the inheritance of inferred haplotypes over the pedigree is consistent without or with allowing for double reduction (DR), and assuming polysomic inheritance.

Usage

pedigreeHapCheck(ped, mrkDosage, haploblock, hapresults)

Arguments

ped	data.frame or matrix listing the pedigree. Column 1 has names of all individuals (no duplicates, no NA), column 2 and 3 have the parents (duplicates and NA allowed, also individuals with one known parent or with two identical parents allowed). No sorting of the pedigree is needed. All parents should also be listed as individuals; if that is not the case the missing parents will be added as founders and a warning will be issued.
mrkDosage	a matrix with one row for each marker and one column for each individual, with the observed dosages. Individuals with one or more NA dosages are considered to have no marker data. Individual names are the colnames, no duplicates allowed; the set of individuals needs not be the same as those in ped; individual names common to mrkDosage and ped must be exactly identical (upper/lower case and whitespace included)
haploblock	a list of character vectors. The names are the names of the haploblocks, the character vectors have the names of the markers in each haploblock
hapresults	a list as returned by inferHaplotypes, with one item per haploblock, containing at least all those in the list specified by haploblock

Value

a list with two items:
- ped_arr: a 3D logical array with dimensions individuals, diagnostics and haploblocks. For each individual and each haploblock there are 4 diagnostics:
* mrk: does the individual have complete marker dosage data?
* imp: were the marker dosages for this individual imputed?
* hap: is there a haplotype combination assigned to the individual?
* noDR: does the haplotype genotype of the individual match that of its parents, assuming polysomic inheritance but no Double Reduction? NA if the individual or both its parents do not have a haplotype genotype assigned
* withDR: as noDR, but allowing Double Reduction
- parents_arr: a 3D integer array with dimensions parents (all individuals that occur as parents in the pedigree), diagnostics and haploblocks. For each parent and each haploblock there are 7 diagnostics:
* par_mrkdata: 0=FALSE, 1=TRUE, does this parent have complete marker data?
* par_hapdata: 0=FALSE, 1=TRUE, does this parent have a haplotype genotype assigned?
* totprogeny: how many first-generation progeny (children) does this parent have (combined over all its matings, both as mother and as father)
* prog_mrkdata: how many progeny have complete marker dosage data?
* prog_hapdata: how many progeny have a haplotype combination assigned?
* nonDRmatch: how many progeny have a haplotype combination that is compatible with their parent's haplotype combinations, assuming polysomic inheritance but no Double Reduction
* DRmatch: as nonDRmatch, but also allowing DR
Both ped_arr and parents_arr contain all haploblocks in haploblock, also those skipped because of too many markers and those without any haplotyped individuals. These can be excluded by excluding them from the haploblock list.

Examples

data(PolyHaplotyper_small)
phchk <- pedigreeHapCheck(ped=phped, mrkDosage=phdos, haploblock=phblocks,
                         hapresults=phresults)
# show the top of the ped_arr for haploblock 1:
phchk$ped_arr[1:6,,1]
# show the top of the parents_arr for haploblock 1:
phchk$parents_arr[1:6,,1]

PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.