IBDmat: Realized IBD relationship

In jendelman/diaQTL: QTL Analysis in Diallel Populations

Realized IBD relationship

Description

Calculates realized relationship matrices from founder genotype probabilities

Usage

IBDmat(
  data,
  dominance = 1,
  epistasis = FALSE,
  spacing = 1,
  chrom = NULL,
  n.core = 1
)

Arguments

data	Variable inheriting from class diallel_geno
dominance	One of 1,2,3,4
epistasis	TRUE/FALSE
spacing	spacing between marker bins, in cM
chrom	Optional, vector of chromosome names to include
n.core	number of cores for parallel execution

Details

Parameter dominance refers to 1 = additive, 2 = digenic, 3 = trigenic, 4 = quadrigenic. Can specify to use only a subset of the chromosomes (by default, all chromosomes are used). If epistasis is TRUE, then dominance must be 1 (additive x additive epistasis). Only pairs of markers on different chromosomes are used for epistasis.

Value

Relationship matrix

Examples

## Not run: 
  IBD_example = IBDmat(data = diallel_example, dominance=1) #additive
  IBD_example = IBDmat(data = diallel_example, dominance=2) #digenic dominance
  IBD_example = IBDmat(data = diallel_example, epistasis=TRUE) #additive x additive epistasis

## End(Not run)

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