overviewByFS: generate an overview of the results by haploblock and by FS...

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

Description

generate an overview of the results by haploblock and by FS family

Usage

overviewByFS(haploblock, parents, FS, hapresults)

Arguments

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.
parents	a matrix of two colums and one row per FS, containing the names of the two parents of each FS
FS	a list of character vectors with the names of the samples for each FS
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:
- ovw: an integer matrix with one row per haploblock and the following columns:
* nmrk: the number of markers in the haploblock
* nhap: the number of different haplotypes assigned over all individuals (NA if no solution was found for this haplotype; the reason for that is listed in the first column of item messages of the return value)
* for each FS family a set of 6 columns:
+ parmrk (0, 1 or 2: the number of parents with complete marker data)
+ fit (0=FALSE or 1=TRUE), indicating if a solution for the FS was found based on polysomic inheritance)
+ mrk: the number of FS progeny with complete marker data
+ imp: the number of FS progeny where complete marker data were imputed
+ hap: the number of FS progeny with assigned haplotype combinations. hap will be less than the mrk value if the same FS marker genotype can be produced with different combinations of haplotypes that are all compatible with the parental haplotype combinations) or if some FS marker genotypes cannot be produced by the inferred parental haplotype combinations
+ P: the chi-squared P-value of the best fitting solution, even if this is discarded because of lack of fit).
* For "rest" (all individuals that are not part of the FS's or their parents) and "all" (all individuals) there are also columns mrk and hap, and for "all" there is also a column imp, similar to those for the FS families. The numbers for "all" are the sums of those for the FS families, the FS parents (some FS may share a parent but shared parents are counted only one) and the "rest".
- messages : a character matrix with one row per haploblock and the following columns:
* haploblock: the reason why there is no solution for the haploblock ("" if there is a solution) * one column for each FS family with a possible message or "". A message can indicate a failure to find a solution for the FS family but may also describe less significant problems, such as some progeny with unexpected marker dosages etc.

Examples

data(PolyHaplotyper_small)
overviewByFS(haploblock=phblocks, parents=phpar, FS=phFS,
            hapresults=phresults)

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