calcStatistics: calculate some statistics of the solutions of all haploblocks

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

Description

calculate some statistics of the solutions of all haploblocks

Usage

calcStatistics(pedchk, ovwFS, indiv, haploblocks)

Arguments

pedchk	a list as generated by pedigreeHapCheck
ovwFS	a list as produced by overviewFS, or NA if no FS families available. If ovwFS is specified, pedchk and ovwFS should have been calculated from the same underlying data
indiv	missing, NULL or a vector of names of individuals. If present, the component pedstats is calculated only over the individuals in the vector, else over all individuals. Component FSstats is not affected by indiv
haploblocks	missing, NULL or a vector of names or numbers of haploblocks, or a list of haploblocks as in the inferHaplotypes input. If present, components pedstats and FSstats are calculated only over the specified haploblocks, else over all haploblocks.

Value

a list with one or two items:
pedstats: a data.frame with one row per haploblock, showing numbers of individuals in columns
- mrk: individuals with complete marker data
- hap: individuals with an assigned haplotype combination
- match.NA: individuals where a match between the haplotypes of the individual and its parents could not be verified (either the individual itself or both parents have no haplotype combination assigned)
- noDR.TRUE: individuals whose haplotype combination matches that of its parents, assuming polysomic inheritance without Double Reduction
- noDR.FALSE: individuals whose haplotype combination doesn't match that of its parents, assuming polysomic inheritance without Double Reduction
- withDR.TRUE: individuals whose haplotype combination matches that of its parents, assuming polysomic inheritance, allowing Double Reduction
- withDR.FALSE: individuals whose haplotype combination doesn't match that of its parents, assuming polysomic inheritance, allowing Double Reduction
The total number of individuals is
match.NA + noDR.TRUE + noDR.FALSE == match.NA + withDR.TRUE + withDR.FALSE;
the number of individuals with missing marker data or without assigned haplotype dosages can be calculated by subtracting mrk or hap from that total.
FSstats (only if ovwFS specified): a data.frame with for each FS family, "rest" and "all" one row, with columns
- pop: the FS family numbers, "rest" (all individuals not belonging to the FSs or their parents) and "all" (all individuals)
- bothparmrk: for how many haploblocks have both parents complete marker data?
- FSdone: for how many haploblocks has a solution based on polysomic inheritance been found for this FS family?
- mrk: the average number of (FS) individuals with complete marker data
- imp: the average number of (FS) individuals with imputed marker data
- hap: the average number of (FS) individuals with an assigned haplotype combination
The numbers for "all" include also the FS parents (each parent counted only once, even if some parents produced more than one FS family), which are not included in any of the other rows; therefore "all" is not equal to the sum of the rows above.

Examples

data(PolyHaplotyper_small)
phchk <- pedigreeHapCheck(ped=phped, mrkDosage=phdos, haploblock=phblocks,
                          hapresults=phresults)
phovw <- overviewByFS(haploblock=phblocks, parents=phpar, FS=phFS,
                     hapresults=phresults)
calcStatistics(pedchk=phchk, ovwFS=phovw)

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