trio: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Version 3.14.0

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

AuthorHolger Schwender, Qing Li, Philipp Berger, Christoph Neumann, Margaret Taub, Ingo Ruczinski
Bioconductor views GeneticVariability Genetics Microarray SNP
Date of publicationNone
MaintainerHolger Schwender <holger.schw@gmx.de>
LicenseLGPL-2
Version3.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("trio")

Popular man pages

colGxGPerms: Permutation-Based gTDT for Two-Way Interactions
colTDTmaxTest: Maximum Genotypic TDT
colTDTsam: SAM and EBAM for Trio Data
getMatPseudo: Generates Case-Pseudo-Control Matrix
trioFS: Trio Feature Selection
trio.power: Power and sample size calculation
trio.prepare: Generate Trio Data Format Suitable for Trio Logic Regression
See all...

All man pages Function index File listing

Man pages

allelicTDT: Allelic TDT
colEMlrt: EM Likelihood Ratio Test
colGxE: Genotypic TDT for Gene-Environment Interactions
colGxGPerms: Permutation-Based gTDT for Two-Way Interactions
colPOlrt: Parent-of-Origin Tests
colTDTmaxTest: Maximum Genotypic TDT
colTDTsam: SAM and EBAM for Trio Data
findLDblocks: Identifying LD blocks
getLD: Computation of LD Measures
getMatPseudo: Generates Case-Pseudo-Control Matrix
lrControl: Control Parameters for Trio Logic Regression
ped2geno: Transformation of Ped-File
plot.getLD: Plotting a getLD or getLDlarge Object
plot.LDblocks: Plotting a LDblock Object
plot.trioLR: Plotting for trioLR Objects
poly4root: Roots of a Fourth Degree Polynomial
print.colGxE: Printing and Storing of colGxE objects
print.trioFS: Printing and plotting of a trioFS object
print.trioLR: Printing of trioLR Objects
probTDT: TDT on genotype probabilities matrix
read.pedfile: Reading a Ped File
removeSNPs: Remove SNPs or Trios
scoreTDT: Score Tests for SNPs, GxE, and GxG Interactions
tdt: Genotypic TDT
tdtGxG: Genotypic TDT for Two-Way Interactions
trio.check: Check Case-Parent Trio Data for Mendelian Errors
trio.data: Case-Parent Trio Data
trioFS: Trio Feature Selection
trioLR: Trio Logic Regression
trio.permTest: Permutation Tests for Trio Logic Regression
trio.power: Power and sample size calculation
trio.prepare: Generate Trio Data Format Suitable for Trio Logic Regression
trio.sim: Simulate Case-Parent Trios
vcf2geno: Transformation of VFC File

Functions

ESp.impu1Par Source code
ESp.impu1Par.A Source code
ESp.impu1Par.A.sp Source code
ESp.impu1Par.B Source code
ESp.impu1Par.B.sp Source code
ESp.impu1Par.C Source code
ESp.impu1Par.C.sp Source code
ESp.impu1Par.D Source code
ESp.impu1Par.D.sp Source code
ESp.impu1Par.E Source code
ESp.impu1Par.E.sp Source code
ESp.impuParent.heterKid Source code
ESp.impuParent.homoKid Source code
ESp.imputBlock Source code
EvsG2 Source code
EvsG2chunk Source code
EvsG2split Source code
EvsG4 Source code
EvsG4chunk Source code
EvsG4split Source code
HRCB.Esp1Rule.sampleKid Source code
HRCB.Esp1Rule.spTrioOnBase Source code
HRCB.applyRule Source code
HRCB.famMap.spTrio Source code
HRCBSpGrp.cons Source code
HRCBSpGrp.sp Source code
LDdata Man page
aTDTchunk Source code
allBetweenCombs Source code
allCombs Source code
allNeighborCombs Source code
allelicTDT Man page Source code
augBkFrame Source code
binaTree.1Level.changeSignal Source code
binaTree.addElm Source code
binaTree.addNode Source code
binaTree.apply Source code
binaTree.closeNode Source code
binaTree.constr Source code
binaTree.merge Source code
binaTree.parser Source code
binaTree.parser.pVarElm Source code
binaTree.parser.proc Source code
binaTree.patternForm Source code
binaTree.patternFormOLD Source code
binaTree.setApply Source code
binaTree.shuffle.findElmPar Source code
binaTree.shuffle.findNodePar Source code
binaTree.shuffleNode Source code
binaTree.toStr Source code
bindHapBkGenoMaps Source code
bkMap.ESp.apply1Rule Source code
bkMap.ESp.apply1Rule.stepBy Source code
bkMap.HRCB.Esp1Rule.Base Source code
bkMap.HRCB.Esp1Rule.genoSeq Source code
bkMap.HRCB.LRCB.split Source code
bkMap.HRCB.famMap Source code
bkMap.LRCB.spTrio Source code
bkMap.constr Source code
bkMap.findHRCBIdx Source code
bkMap.genoFreq Source code
bkMap.shuffle Source code
bkMap.spGenoSeq Source code
bkMap.spHap Source code
bkMap.superHRCB Source code
bkMap.updateByRule Source code
bkMap.updateHapFreq Source code
bothHet Source code
bothHetMat Source code
calHapIdx2SHap Source code
calHapIdx2SHapSet Source code
casusIrred Source code
checkControlPars Source code
checkMendelianError Source code
checkTLRinput Source code
chunkGenoCombAdd Source code
chunkGenoCombDom Source code
chunkGenoCombRec Source code
colEMlrt Man page Source code
colGxE Man page Source code
colGxEPerms Man page Source code
colGxEunstructured Source code
colGxG Man page Source code
colGxGPerms Man page Source code
colGxGlrt Source code
colMAFtrio Man page Source code
colPOlrt Man page Source code
colTAT Man page Source code
colTDT Man page Source code
colTDT2way Man page Source code
colTDTebam Man page Source code
colTDTepistatic Source code
colTDTinter2way Man page Source code
colTDTmaxStat Man page Source code
colTDTmaxTest Man page Source code
colTDTsam Man page Source code
comp2MatX11 Source code
compBothHet Source code
compD Source code
compFailTDT Source code
compFailTDTmax Source code
compLDsplit Source code
compPermTDT2way Man page Source code
compVarDprime Source code
compVarEvsG2 Source code
compVarEvsG4 Source code
compX11 Source code
covDipBinaMa2CodedGeno Source code
covDipStr2CodedGeno Source code
derivExpit Source code
derivLLadd Source code
derivLLdom Source code
derivLLrec Source code
dfToGenoMap Source code
dfToHapBkMap Source code
em.step.both Source code
em.step.father Source code
em.step.mother Source code
est.pAB Source code
est.pAB2Mat Source code
estimateRatioTDT Source code
exDipProbSemiAugMap Source code
exIdxFromHap Source code
exParentDip Source code
exchangeDigit Source code
exhaustHapExp Source code
fHapBkIdx2DipTb Source code
fastGxEdomSplit Source code
fastGxErecSplit Source code
fastGxEsplit Source code
fastGxG Man page Source code
fastGxGrec Man page Source code
fastTDT Source code
fastTDTchunk Source code
fastTDTdomChunk Source code
fastTDTdomSplit Source code
fastTDTrecChunk Source code
fastTDTrecSplit Source code
fastTDTsplit Source code
filterHapIdx2SuperHapSet Source code
filterHaps2SHaps Source code
filterHaps2SHaps.check Source code
find.PsudoControlHap Source code
findLDblocks Man page Source code
findLastPreviousDate Source code
findMissing Source code
freq.allele Source code
freq.build Source code
freq.hap Man page
freqbuild.haponly Source code
freqmap.reconstruct Source code
genGenoProb Source code
genMatingTBCondOnChild3 Source code
geno.2dStr2BinaMa Source code
geno2hapFreq Source code
getBackParentGeno Source code
getBetaAdd Source code
getBetaDom Source code
getBetaRec Source code
getBetaRec2 Source code
getCalls4LD Source code
getDummyX Source code
getGenoComb Source code
getGxENullStats Source code
getGxEstats Man page Source code
getHapProb.semiMapFrame Source code
getHapProb2 Source code
getLD Man page Source code
getLDlarge Man page Source code
getLogRoot Source code
getMatPseudo Man page Source code
getNullStats Source code
getOriginalStat Source code
getP.logodds Source code
getPOlrtCounts Source code
getPermStat Source code
getSNPdummyNames Source code
getScoresChunk Source code
getStatsChunk Source code
getTATnumbers Source code
getYmat Source code
grp.CI Source code
grp.kmStep Source code
grp.palette Source code
gtdt.ebam Man page Source code
gtdt.null.add Source code
gtdt.null.approx Source code
gtdt.null.approx2 Source code
gtdt.null.dom Source code
gtdt.null.rec Source code
gtdt.null.samp Source code
gtdt.stat Man page Source code
gxe.null.stats Source code
gxeBetaVadd Source code
gxeBetaVdom Source code
gxeBetaVrec Source code
hap.2geno Source code
hap2GenoBlock Source code
hap2genotype.bk Source code
hap2genotype.m Source code
hapBk2AlleleSeq Source code
hapBkGenoMap2HapMap Source code
hapGenoBlockProc Source code
hapPair.match Source code
impuBk.scheduler Source code
impuBkTDT.scheduler Source code
imputGeno Source code
isDigitAtLociIdx Source code
linkageFile.proc Source code
listExtractor Source code
llEvsG2 Source code
llEvsG4 Source code
logBe Source code
logErr Source code
logWarn Source code
loge Source code
logit Source code
logl Source code
logs Source code
lrControl Man page Source code
lrtGxE Source code
lrtGxEdom Source code
lrtGxErec Source code
ls.list Source code
mat.test Man page
matTBCondOnChild3.finalProc Source code
maxStatEBAM Source code
maxStatSAM Source code
moveDir Source code
negPOfullLike Source code
negPOredLike Source code
neighborCombs Source code
neighborIds Source code
noBothHet Source code
noBothHetMat Source code
onAttach Source code
orderSNPs Man page Source code
ped2geno Man page Source code
plot.LDblocks Man page Source code
plot.getLD Man page Source code
plot.getLDlarge Man page Source code
plot.trioFS Man page Source code
plot.trioLR Man page Source code
plotTrioTree Source code
polrtChunk Source code
poly4root Man page Source code
poly4rootMat Man page Source code
predLL Source code
print.LDblock Man page
print.LDblocks Source code
print.aTDT Man page Source code
print.colEMlrt Man page Source code
print.colGxE Man page Source code
print.colGxEunstruct Man page Source code
print.colTDT Man page Source code
print.colTDTepi Man page Source code
print.maxScoreTrio Man page Source code
print.maxStatTrio Man page Source code
print.maxTestTrio Man page Source code
print.polrt Man page Source code
print.scoreGxE Man page Source code
print.scoreTDT Man page Source code
print.tat Man page Source code
print.tdt Man page Source code
print.tdtEpi Man page Source code
print.trio.power Man page Source code
print.trioFS Man page Source code
print.trioLR Man page Source code
printTrioTree Source code
prob.mat.test Man page
probTDT Man page Source code
probTDTchunk Source code
probTDTdomChunk Source code
probTDTdomSplit Source code
probTDTrecChunk Source code
probTDTrecSplit Source code
probTDTsplit Source code
procSemiAugMap Source code
qExpandTable Source code
qStr.pattern Source code
qTraceback Source code
qing.cut Source code
qing.mulMatch Source code
qp Source code
qstrsplit Source code
read.pedfile Man page Source code
removeKids Source code
removeSNPs Man page Source code
removeTrios Man page Source code
reorderEnv Source code
resample Source code
rootBeta Source code
rootCasusIrr Source code
rootRleq0 Source code
sam.Hap.old Source code
sam.reject Source code
sampleDipSemiAugMap Source code
sampleHapExclude Source code
sampleHapSemiAugMap2 Source code
sampleIdxOutsideList Source code
scoreBetaAdd Source code
scoreBetaDom Source code
scoreBetaRec Source code
scoreGxE Man page Source code
scoreGxEdomSplit Source code
scoreGxErecSplit Source code
scoreGxEsplit Source code
scoreGxG Man page Source code
scoreMaxStat Man page Source code
scoreTDT Man page Source code
scoreTDTchunk Source code
scoreTDTdomChunk Source code
scoreTDTdomSplit Source code
scoreTDTrecChunk Source code
scoreTDTrecSplit Source code
scoreTDTsplit Source code
semiAugBkFrame Source code
setTrioMissingSNP Source code
signal.new Source code
signalRule.2strata.build Source code
signalRule.addSignal Source code
signalRule.contr Source code
signalRule.setInter Source code
simuBkMap Man page
simuHapMap.build Source code
snpPREFileMatchTrio Source code
splitBlock Source code
splitBlocks Man page Source code
step3way Man page
tatChunk Source code
tdt Man page Source code
tdt2way Man page Source code
tdtEpistatic Source code
tdtGxG Man page Source code
toolbox.load Source code
trio.check Man page Source code
trio.data Man page
trio.gen.err Man page
trio.gen1 Man page
trio.gen2 Man page
trio.impu Source code
trio.impuDev Source code
trio.match.single Source code
trio.ped.err Man page
trio.ped1 Man page
trio.ped2 Man page
trio.permTest Man page Source code
trio.power Man page Source code
trio.prepare Man page Source code
trio.sim Man page Source code
trio.simu.direct Source code
trio.simu.proposed Source code
trio.simuDev Source code
trio.simuOLD Source code
trioBagging Source code
trioFS Man page Source code
trioFS.default Man page Source code
trioFS.formula Man page Source code
trioFS.trioPrepare Man page Source code
trioFile.proc Source code
trioLR Man page Source code
trioLR.default Man page Source code
trioLR.formula Man page Source code
trioLR.trioPrepare Man page Source code
trioMerge Source code
trioPImp Source code
trioPImpEval Source code
triologreg Source code
txtToGenoMap Source code
txtToHapBkMap Source code
util.array.rmEmptyStr Source code
util.array3d.2matrix Source code
util.char.1stIdx Source code
util.char.1stStrIdx Source code
util.dataframe.findColNo Source code
util.dataframe.merge Source code
util.dataframe.round Source code
util.findBrace Source code
util.it.smallLargeIdx Source code
util.it.smallLargeIdxOOLD Source code
util.it.triMatch Source code
util.it.triMatch2 Source code
util.it.upTriCombIdx Source code
util.list.2matrix Source code
util.list.ex Source code
util.list.rmByKeyVal Source code
util.listMatrix.2matrix Source code
util.matrix.2list Source code
util.matrix.cat Source code
util.matrix.catSave Source code
util.matrix.catm Source code
util.matrix.clone Source code
util.matrix.col.shuffle Source code
util.matrix.col.shuffle2 Source code
util.matrix.colComp Source code
util.matrix.colIdx4Match Source code
util.matrix.csvText Source code
util.matrix.delCol Source code
util.matrix.exByKeyInRow Source code
util.matrix.insertCol Source code
util.matrix.merge Source code
util.matrix.rmSparseRow Source code
util.randomCaseAssign Source code
util.shuffleIdx Source code
util.sql.groupby Source code
util.str.2CharArray Source code
util.str.replace Source code
util.str.rmSpacePadder Source code
util.str.seqCutter Source code
util.str.splitAndOrNot Source code
util.str.splitEx Source code
util.str.tokenPicker Source code
util.tbl.exFactorInfo Source code
util.vec.2maIdx Source code
util.vec.exByKey Source code
util.vec.matchVec Source code
util.vec.matchVecIdx Source code
util.vec.orderPair Source code
util.vec.replace Source code
valDeriv2LLadd Source code
vcf2geno Man page Source code
vim.trioFS Source code
vimTrio Source code
vimTrio.oneprime Source code
vt1 Source code
vt1r Source code
vt2 Source code
vt2r Source code
vt3 Source code
vt3r Source code
vt4 Source code
vt4r Source code
wrComTbl Source code

Files

DESCRIPTION
NAMESPACE
R
R/allelicTDT.R
R/colEMlrt.R
R/colGxE.R
R/colGxEPerms.R
R/colGxGperm.R
R/colMAFtrio.R
R/colPOlrt.R
R/colTAT.R
R/colTDTmaxTest.R
R/colTDTsam.R
R/fastGxG.R
R/fastTDT.R
R/getLD.R
R/getLDlarge.R
R/lrControl.R
R/ped2geno.R
R/poly4root.R
R/probTDT.R
R/qingInternal.R
R/read.pedfile.R
R/removeSNPs.R
R/scoreTDT.R
R/splitBlocks.R
R/tdt.R
R/trio.R
R/trio.check.R
R/trio.permTest.R
R/trio.power.R
R/trio.sim.R
R/trioFS.R
R/trioLR.R
R/triologreg.R
R/vcf2geno.R
R/zzz.R
build
build/vignette.rds
data
data/trio.data.RData
inst
inst/doc
inst/doc/trio.R
inst/doc/trio.Rnw
inst/doc/trio.pdf
man
man/allelicTDT.Rd
man/colEMlrt.Rd
man/colGxE.Rd
man/colGxGPerms.Rd
man/colPOlrt.Rd
man/colTDTmaxTest.Rd
man/colTDTsam.Rd
man/findLDblocks.Rd
man/getLD.Rd
man/getMatPseudo.Rd
man/lrControl.Rd
man/ped2geno.Rd
man/plot.LDblocks.Rd
man/plot.getLD.Rd
man/plot.trioLR.Rd
man/poly4root.Rd
man/print.colGxE.Rd
man/print.trioFS.Rd
man/print.trioLR.Rd
man/probTDT.Rd
man/read.pedfile.Rd
man/removeSNPs.Rd
man/scoreTDT.Rd
man/tdt.Rd
man/tdtGxG.Rd
man/trio.check.Rd
man/trio.data.Rd
man/trio.permTest.Rd
man/trio.power.Rd
man/trio.prepare.Rd
man/trio.sim.Rd
man/trioFS.Rd
man/trioLR.Rd
man/vcf2geno.Rd
vignettes
vignettes/figure1ld.eps
vignettes/figure1ld.png
vignettes/figure1lr.eps
vignettes/figure1lr.png
vignettes/figure2ld.eps
vignettes/figure2ld.png
vignettes/figure2lr.eps
vignettes/figure2lr.png
vignettes/figure3ld.eps
vignettes/figure3ld.png
vignettes/figure3lr.eps
vignettes/figure3lr.png
vignettes/qingSweave.sty
vignettes/trio.Rnw
trio documentation built on May 20, 2017, 9:52 p.m.

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