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

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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 <riyan.cheng@anu.edu.au>
Date of publication
2015-11-12 08:42:52
Maintainer
Riyan Cheng <riyan.cheng@anu.edu.au>
License
GPL (>= 2)
Version
0.2-15

View on CRAN

Man pages

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
plots
Plotting
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

Files in this package

QTLRel
QTLRel/inst
QTLRel/inst/CITATION
QTLRel/inst/doc
QTLRel/inst/doc/index.html
QTLRel/inst/doc/QTLRel_Tutorial.R
QTLRel/inst/doc/QTLRel_Tutorial.pdf
QTLRel/src
QTLRel/src/qqplot.c
QTLRel/src/ks.c
QTLRel/src/imFn.c
QTLRel/src/ibsFn.c
QTLRel/src/rgdat.c
QTLRel/src/xxx.h
QTLRel/src/idcoef.c
QTLRel/NAMESPACE
QTLRel/data
QTLRel/data/miscEx.RData
QTLRel/R
QTLRel/R/scan.R
QTLRel/R/idcoef.R
QTLRel/R/estVC.R
QTLRel/R/aic.R
QTLRel/R/pedRecode.R
QTLRel/R/qtl2rel.R
QTLRel/R/imFn.R
QTLRel/R/qqPlot.R
QTLRel/R/plots.R
QTLRel/R/ibsFn.R
QTLRel/R/herit.R
QTLRel/R/rem.R
QTLRel/R/rel2qtl.R
QTLRel/R/nullSim.R
QTLRel/R/hapSim.R
QTLRel/R/lodci.R
QTLRel/R/zzz.R
QTLRel/MD5
QTLRel/DESCRIPTION
QTLRel/ChangeLog
QTLRel/man
QTLRel/man/nullSim.Rd
QTLRel/man/aicVC.Rd
QTLRel/man/genoProb.Rd
QTLRel/man/rel2qtl.Rd
QTLRel/man/lodci.Rd
QTLRel/man/qqplot.Rd
QTLRel/man/hapSim.Rd
QTLRel/man/mAIC.Rd
QTLRel/man/qtlVar.Rd
QTLRel/man/estVC.Rd
QTLRel/man/genMatrix.Rd
QTLRel/man/blup.Rd
QTLRel/man/scanTwo.Rd
QTLRel/man/miscEx.Rd
QTLRel/man/qtl2rel.Rd
QTLRel/man/cic.Rd
QTLRel/man/ibs.Rd
QTLRel/man/kinship.Rd
QTLRel/man/scanOne.Rd
QTLRel/man/misFct.Rd
QTLRel/man/genoImpute.Rd
QTLRel/man/plots.Rd
QTLRel/man/genoSim.Rd
QTLRel/man/gls.Rd
QTLRel/man/rem.Rd
QTLRel/man/pedRecode.Rd