diallel_geno_pheno-class: S4 class with genotype and phenotype data

In jendelman/diaQTL: QTL Analysis in Diallel Populations

S4 class with genotype and phenotype data

Description

S4 class with genotype and phenotype data

Slots

ploidy

Either 2 or 4

input

matrix of character strings from the genotype input file

Xa

list of matrices with the expected haplotype dosage (rows) for each parental origin genotype (columns)

dominance

Maximum dosage stored in slot geno. Integer 1-4 indicating 1 = additive, 2 = digenic dominance, 3 = trigenic dominance, 4 = quadrigenic dominance.

X.GCA

Incidence matrix for GCA effects

map

data frame with marker,chrom, position (cM and/or bp) and bin

geno

list of length equal to the number of marker bins. Each element is a list of length dominance. The elements in the nested list are sparse matrices with dimensions (id x effects), containing the dosage for each effect.

A

list with the additive relationship matrix for each chromosome

pheno

data frame of phenotypes

X

incidence matrix for fixed effects

Z

incidence matrix for individuals

jendelman/diaQTL documentation built on Jan. 27, 2024, 6:39 a.m.