showOneFS: show marker and haplotype dosages for one FS family

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

Description

show marker and haplotype dosages for one FS family and its parents

Usage

showOneFS(FSnr, hbresults, mrkDosage, FS, parents)

Arguments

FSnr	the number of the FS family (indexes the FS list and parents)
hbresults	a list with the haplotyping results for one haploblock: one element of a list as returned by inferHaplotypes
mrkDosage	a matrix of marker dosages, may contain rows for more markers than only those in the current haploblock (the relevant markers are specified in the hbresults list)
FS	a list of which each item is a (character) vector with the names of the individuals in that FS family
parents	a (character) matrix with 2 columns and one row for each FS family in FS, with the names of the two parents of each family

Value

a list with 3 elements:
$mrkdat: a matrix with info on the marker dosages distribution in the FS. The first two columns are for the parents: the parent name is between (brackets) in the column name, their mrkdid (marker dosage ID) in row 1 and their marker dosages below that. The remaining columns are for the different mrkdids observed in the FS: the mrkdid itself in the column name, its frequency in row 1 and its marker dosages below that. The final column gives the frequency of individuals with one or more missing marker dosages.
$hapdat: a matrix with similar layout as mrkdat, but now with the haplotype dosages rather than the marker dosages. Some mrkdids (columns) may not have a haplotype dosage combination assigned (if multiple possible haplotype combinations result in the same marker dosages)
usedhap: a matrix with the dosage (0 or 1) of each marker in each of the used haplotypes; haplotype nrs in columns, markers in rows

Examples

data(PolyHaplotyper_small)
# show the results of the first FS family in the first haploblock:
showOneFS(FSnr=1, hbresults=phresults[[1]], mrkDosage=phdos,
         FS=phFS, parents=phpar)

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