Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees
AIC Model Selection
Best Linear Unbiased Prediction
Calculate Jacquard condensed identity coefficients
Spectral decomposition of a matrix
Estimate Variance Component Parameters
Derive genetic matrices
Impute Genotypic Data
Probability of a Genotype.
Generate Genotypic Data
Generalized Least Squares Estimates
Generate Genotypic Data
Estimate Jacquard condensed identity coefficients
Calculate kinship coefficients
Estimate LOD Support Intervals
Multiple QTL AIC
A collection of other functions.
Simulate null distribution
Recode a Pedigree
Plotting
Quantile-Quantile Plots
Convert data from R/qtl to QTLRel format
QTL Variance
Convert data from QTLRel to R/qtl format
Random effect matrices
Genome Scan for QTL
Genome Scan for Epistasis
This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.