API for trio
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
| Global functions | |
|---|---|
| .onAttach | Source code |
| 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 |
| 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.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.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 |
| logit | 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 |
| 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 |
| 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.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.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 |
