QTLRel: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees
Version 0.2-15

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.

Browse man pages Browse package API and functions Browse package files

AuthorRiyan Cheng <riyan.cheng@anu.edu.au>
Date of publication2015-11-12 08:42:52
MaintainerRiyan Cheng <riyan.cheng@anu.edu.au>
LicenseGPL (>= 2)
Version0.2-15
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("QTLRel")

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

Functions

AICb Source code
AICb.HK Source code
AICf Source code
AICf.HK Source code
AICmove Source code
AICmove.HK Source code
Fn Source code
Fn. Source code
Fn.0 Source code
W.inv Source code
aicVC Man page Source code
aicVC.default Source code
aicVCb Source code
aicVCf Source code
ans Source code
blup Man page Source code
blup.aic Source code
blup.bgv Source code
cic Man page Source code
cicTmp Source code
estRR Source code
estVC Man page Source code
estVC.1 Source code
estVC.2 Source code
estVC.3 Source code
estVC.4 Source code
estVC.default Source code
fci Source code
flod Source code
fmaxSize Source code
fn2 Source code
fn2s Source code
fn3 Source code
fn4 Source code
fn4.2 Source code
fns4.2 Source code
freeSpace Source code
fs2n Source code
fv Man page Source code
fxx.hk Source code
gdatF8 Man page
genMatrix Man page Source code
genMatrix.cic Source code
genMatrix.default Source code
genoImpute Man page Source code
genoImpute.Pr Source code
genoImpute.default Source code
genoPos Man page Source code
genoPr0 Source code
genoPr1 Source code
genoProb Man page Source code
genoProb.default Source code
genoSim Man page Source code
gls Man page Source code
gmF8 Man page
gmapF8 Man page
gvar Man page Source code
hapSim Man page Source code Source code
hapSim0 Source code
ibs Man page Source code
ibs.1 Source code
ibs.2 Source code
is.ll Source code
kinship Man page Source code
lmGls Source code
lodci Man page Source code Source code
mAIC Man page Source code
mAIC.HK Man page Source code
mAIC.default Source code
mappingFunc Source code
mappingFuncInv Source code
miscEx Man page
nullSim Man page Source code
onAttach Source code
onUnload Source code
pdatF8 Man page
ped.local.no Source code
ped.opt Source code
pedF8 Man page
pedRecode Man page Source code
pedRecode.0 Source code
pk Source code
pkolm Man page Source code
plot Man page
plot.lrt Source code
plot.scanOne Man page Source code
plot.scanTwo Man page Source code
plotit Man page Source code
print.aic Source code
print.bgv Source code
print.scanOne Source code
qFn Source code
qFn. Source code
qk Source code
qkolm Man page Source code
qqPlot Man page Source code
qqPlot.default Source code
qtl2rel Man page Source code
qtlVar Man page Source code
rFn Source code
rel2qtl Man page Source code
rem Man page Source code
rem.1 Source code
rem.2 Source code
root Source code
scanOne Man page Source code
scanOne.0 Source code
scanOne.1 Source code
scanOne.2 Source code
scanOne.default Source code
scanTwo Man page Source code
scanTwo.1 Source code
scanTwo.2 Source code
scanTwo.default Source code
smpl Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/index.html
inst/doc/QTLRel_Tutorial.R
inst/doc/QTLRel_Tutorial.pdf
src
src/qqplot.c
src/ks.c
src/imFn.c
src/ibsFn.c
src/rgdat.c
src/xxx.h
src/idcoef.c
NAMESPACE
data
data/miscEx.RData
R
R/scan.R
R/idcoef.R
R/estVC.R
R/aic.R
R/pedRecode.R
R/qtl2rel.R
R/imFn.R
R/qqPlot.R
R/plots.R
R/ibsFn.R
R/herit.R
R/rem.R
R/rel2qtl.R
R/nullSim.R
R/hapSim.R
R/lodci.R
R/zzz.R
MD5
DESCRIPTION
ChangeLog
man
man/nullSim.Rd
man/aicVC.Rd
man/genoProb.Rd
man/rel2qtl.Rd
man/lodci.Rd
man/qqplot.Rd
man/hapSim.Rd
man/mAIC.Rd
man/qtlVar.Rd
man/estVC.Rd
man/genMatrix.Rd
man/blup.Rd
man/scanTwo.Rd
man/miscEx.Rd
man/qtl2rel.Rd
man/cic.Rd
man/ibs.Rd
man/kinship.Rd
man/scanOne.Rd
man/misFct.Rd
man/genoImpute.Rd
man/plots.Rd
man/genoSim.Rd
man/gls.Rd
man/rem.Rd
man/pedRecode.Rd
QTLRel documentation built on May 20, 2017, 3:31 a.m.