tetra.solcap.geno.dist: Autotetraploid potato dataset with genotype probabilities.

In mappoly: Genetic Linkage Maps in Autopolyploids

Autotetraploid potato dataset with genotype probabilities.

Description

A dataset of the B2721 population which derived from a cross between two tetraploid potato varieties: Atlantic × B1829-5. The population comprises 160 offsprings genotyped with the SolCAP Infinium 8303 potato array. The original data set can be found in [The Solanaceae Coordinated Agricultural Project (SolCAP) webpage](http://solcap.msu.edu/potato_infinium.shtml) The dataset also contains the genomic order of the SNPs from the Solanum tuberosum genome version 4.03. The genotype calling was performed using the fitPoly R package. Although this dataset contains the probability distribution of the genotypes, it is essentially the same dataset found in tetra.solcap

Usage

tetra.solcap.geno.dist

Format

An object of class mappoly.data which contains a list with the following components:

ploidy

ploidy level = 4

n.ind

number individuals = 160

n.mrk

total number of markers = 4017

ind.names

the names of the individuals

mrk.names

the names of the markers

dosage.p1

a vector containing the dosage in parent P for all n.mrk markers

dosage.p2

a vector containing the dosage in parent Q for all n.mrk markers

chrom

a vector indicating which sequence each marker belongs. Zero indicates that the marker was not assigned to any sequence

genome.pos

Physical position of the markers into the sequence

prob.thres = 0.95

probability threshold to associate a marker call to a dosage. Markers with maximum genotype probability smaller than 'prob.thres' are considered as missing data for the dosage calling purposes

geno

a data.frame containing the probability distribution for each combination of marker and offspring. The first two columns represent the marker and the offspring, respectively. The remaining elements represent the probability associated to each one of the possible dosages

geno.dose

a matrix containing the dosage for each markers (rows) for each individual (columns). Missing data are represented by ploidy_level + 1 = 5

n.phen

There are no phenotypes in this simulation

phen

There are no phenotypes in this simulation

mappoly documentation built on Jan. 6, 2023, 1:16 a.m.