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.
|Author||Riyan Cheng <firstname.lastname@example.org>|
|Date of publication||2015-11-12 08:42:52|
|Maintainer||Riyan Cheng <email@example.com>|
|License||GPL (>= 2)|
aicVC: AIC Model Selection
blup: Best Linear Unbiased Prediction
cic: Calculate Jacquard condensed identity coefficients
estVC: Estimate Variance Component Parameters
genMatrix: Derive genetic matrices
genoImpute: Impute Genotypic Data
genoProb: Probability of a Genotype.
genoSim: Generate Genotypic Data
gls: Generalized Least Squares Estimates
hapSim: Generate Genotypic Data
ibs: Estimate Jacquard condensed identity coefficients
kinship: Calculate kinship coefficients
lodci: Estimate LOD Support Intervals
mAIC: Multiple QTL AIC
miscEx: Genotype data, phenotype data, genetic map and pedigree.
misFct: A collection of other functions.
nullSim: Simulate null distribution
pedRecode: Recode a Pedigree
qqplot: Quantile-Quantile Plots
qtl2rel: Convert data from R/qtl to QTLRel format
qtlVar: QTL Variance
rel2qtl: Convert data from QTLRel to R/qtl format
rem: Random effect matrices
scanOne: Genome Scan for QTL
scanTwo: Genome Scan for Epistasis