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QTLRel

Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

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.

Functions (27)

AIC Model Selection

blup

Best Linear Unbiased Prediction

cic

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

gls

Generalized Least Squares Estimates

Generate Genotypic Data

ibs

Estimate Jacquard condensed identity coefficients

Calculate kinship coefficients

Estimate LOD Support Intervals

mAIC

Multiple QTL AIC

A collection of other functions.

Genotype data, phenotype data, genetic map and pedigree.

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

rem

Random effect matrices

Genome Scan for QTL

Genome Scan for Epistasis

QTLRel

Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

v1.11

GPL (>= 2)

Authors

Riyan Cheng [aut, cre]

Initial release

2022-6-17

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