API for CGEN
An R package for analysis of case-control studies in genetic epidemiology
| Global functions | |
|---|---|
| CGEN | Man page |
| GC.adj.pvalues | Source code |
| GxE.call.1 | Source code |
| GxE.scan | Man page Source code |
| GxE.scan.1 | Source code |
| GxE.scan.1_2 | Source code |
| GxE.scan.2 | Source code |
| GxE.scan.3 | Source code |
| GxE.scan.3a | Source code |
| GxE.scan.4 | Source code |
| GxE.scan.combine | Man page Source code |
| GxE.scan.genfile | Source code |
| GxE.scan.jobsFile | Source code |
| GxE.scan.partition | Man page Source code |
| GxE.setup.1 | Source code |
| GxE.setup.1_2 | Source code |
| GxE.setup.2 | Source code |
| GxE.setup.3 | Source code |
| GxE.setup.3a | Source code |
| GxE.setup.4 | Source code |
| LocusMapData | Man page |
| Manhattan.plot | Man page Source code |
| Modified_Wald_Test | Source code |
| OR.getTitle | Source code |
| OR.given.E | Source code |
| OR.plot.main | Source code |
| OR.plot.type | Source code |
| OR.plot.type.method | Source code |
| OR_add.LT | Source code |
| OR_add.LT.tmp | Source code |
| Pdg.xs.strat.dom | Source code |
| QQ.plot | Man page Source code |
| QQ.plot2 | Source code |
| QQ.plot_old0 | Source code |
| RERI.AP.S | Source code |
| RERI.AP.S_retro | Source code |
| SAS2Format | Source code |
| UML_CML_GxE_parms | Source code |
| Xdata | Man page |
| addColumn | Source code |
| addInterVars | Source code |
| addIntercept | Source code |
| addLineSegments | Source code |
| addMissingSNPs | Source code |
| additive.test | Man page Source code |
| additiveTest | Source code |
| additiveTest.small | Source code |
| applyFormulas | Source code |
| apply_zero.vars | Source code |
| blockDiag | Source code |
| callGLM | Source code |
| callOS | Source code |
| ccmatch | Source code |
| changeAlleles | Source code |
| changeGenotypes | Source code |
| changeLevels.var | Source code |
| changeStr.names | Source code |
| changeStrata | Source code |
| check.GLU | Source code |
| check.PLINK | Source code |
| check.file.list | Source code |
| check.files | Source code |
| check.include.snps | Source code |
| check.list.vec.char | Source code |
| check.locusMap.list | Source code |
| check.pheno.list | Source code |
| check.snp.list | Source code |
| check.subject.list | Source code |
| check.subsetData.list | Source code |
| check.temp.list | Source code |
| check.vec | Source code |
| check.vec.char | Source code |
| check.vec.num | Source code |
| checkBaseModel | Source code |
| checkDelimiter | Source code |
| checkForConstantVar | Source code |
| checkForSep | Source code |
| checkPheno.vars | Source code |
| checkTryError | Source code |
| checkVars | Source code |
| chrm.plot.colors | Source code |
| chrm.plot.legend | Source code |
| chrm.plot.main | Source code |
| chrm.plot.pch | Source code |
| chrm.plot.ylim | Source code |
| closeFile | Source code |
| convertParams3 | Source code |
| create.formula | Source code |
| createDummy | Source code |
| createScript | Source code |
| crossTab | Source code |
| dat2rda | Source code |
| debug.time | Source code |
| default.list | Source code |
| dsgnMat | Source code |
| effScoreVar_small | Source code |
| effScoreVar_small.split.indep2 | Source code |
| effScoreVar_small.split2 | Source code |
| effects.init | Source code |
| exportSAS | Source code |
| extract.SNP.file | Source code |
| extract.SNP.vec | Source code |
| extract.SNPinfo.vec | Source code |
| extractByStr | Source code |
| extractEst | Source code |
| extractVar.general | Source code |
| extract_UML.CML | Source code |
| factorVars | Source code |
| findRoot.optim.binary | Source code |
| findRoot.optim.binary2 | Source code |
| freqCounts.var | Source code |
| gene.getOrder | Source code |
| gene.plot | Source code |
| gene.plot.colors | Source code |
| gene.plot.main | Source code |
| gene.transform.loc | Source code |
| genfile.list | Source code |
| genfile.vec | Source code |
| get.EB.A_matrix | Source code |
| get.in.miss | Source code |
| get.nsnps.vec | Source code |
| getAllVars | Source code |
| getAllVars.pheno | Source code |
| getBetaObject | Source code |
| getCI | Source code |
| getColNumber | Source code |
| getColors | Source code |
| getColsFromCharVec | Source code |
| getColumns | Source code |
| getCommandArg | Source code |
| getCov12Object | Source code |
| getCovObject | Source code |
| getData.1 | Source code |
| getDelimiter | Source code |
| getDesignMatrix | Source code |
| getEstCov | Source code |
| getExtremeSubs | Source code |
| getFID | Source code |
| getFigs | Source code |
| getFileDelim | Source code |
| getFileHeader | Source code |
| getFilePtr | Source code |
| getFilePtr.genoFile | Source code |
| getFileType | Source code |
| getFormulas | Source code |
| getGenoCounts | Source code |
| getGenoStats | Source code |
| getIds.file | Source code |
| getIdsFromFile | Source code |
| getInheritanceVec | Source code |
| getInteractions | Source code |
| getLims | Source code |
| getLinearComb.var | Source code |
| getListName | Source code |
| getLocusMap | Source code |
| getLoglike.glm | Source code |
| getLoglike.mat | Source code |
| getMAF | Source code |
| getMAF.control | Source code |
| getMatchedSets | Man page Source code |
| getModelData | Source code |
| getNames | Source code |
| getNcols | Source code |
| getNextObs | Source code |
| getNextObs.stream | Source code |
| getNrows | Source code |
| getNumGenoVec | Source code |
| getOR.CI | Source code |
| getORfromLOR | Source code |
| getOrder | Source code |
| getPermutation | Source code |
| getPermutation.strata | Source code |
| getPheno.file | Source code |
| getPheno.info | Source code |
| getPhenoData | Source code |
| getPhenoGeno.ids | Source code |
| getPhenoGeno.stream | Source code |
| getRR.general | Source code |
| getRead.n | Source code |
| getRow1.omitN | Source code |
| getSASData | Source code |
| getSNPinfo.vec | Source code |
| getSNPsToInclude | Source code |
| getSnpLoadList | Source code |
| getSnpNames | Source code |
| getSubIds.genoFile | Source code |
| getSubjIds | Source code |
| getSubject.vec | Source code |
| getSubsToInclude | Source code |
| getSubsetDataVars | Source code |
| getSummary | Man page Source code |
| getSummary.main | Source code |
| getTempfile | Source code |
| getUniqueChrm | Source code |
| getUniqueVarName | Source code |
| getValue.cvec | Source code |
| getVarNames | Source code |
| getVarNames.int | Source code |
| getVarNames.snp | Source code |
| getVecFromStr | Source code |
| getWaldTest | Man page Source code |
| getXBeta | Source code |
| getZ.datX.general | Source code |
| getZ.dom | Source code |
| getZ.general | Source code |
| ginfo.GLU | Source code |
| glu.LD.snps | Source code |
| glu.SNP_bins | Source code |
| glu.commonSNPs | Source code |
| glu.create_ped | Source code |
| glu.extract | Source code |
| glu.getCounts | Source code |
| glu.ginfo | Source code |
| glu.ldMatrix | Source code |
| glu.mergeAlleles | Source code |
| glu.mergePhenoGeno | Source code |
| glu.nBins | Source code |
| glu.partition | Source code |
| glu.qcsummary | Source code |
| glu.r2 | Source code |
| glu.renameAlleles | Source code |
| glu.snps_in_genes | Source code |
| glu.transform | Source code |
| her2.log | Source code |
| heterTest | Source code |
| impute.R2.GLU.file | Source code |
| impute.R2.file | Source code |
| impute.find_files | Source code |
| impute.get_SNP | Source code |
| impute.get_data | Source code |
| impute.get_genoVec | Source code |
| impute.get_probVecs | Source code |
| impute.get_value | Source code |
| impute.get_value.str | Source code |
| impute.get_vec | Source code |
| impute.gmodel | Source code |
| impute.maxProbGeno | Source code |
| impute.mergePhenoGeno | Source code |
| impute.toLDAT.file | Source code |
| impute.toLDAT.str | Source code |
| impute.toTPED.file | Source code |
| impute.toTPED.str | Source code |
| inflationFactor | Source code |
| info.small.add2 | Source code |
| info.small.standard | Source code |
| info.small_probit | Source code |
| initDataFrame | Source code |
| intersectSubIds | Source code |
| likelihoodRatio | Source code |
| likelihoodRatio.main | Source code |
| load.impute2 | Source code |
| loadData | Source code |
| loadData.stream | Source code |
| loadData.table | Source code |
| loadData.type1 | Source code |
| loadFile | Source code |
| locusMap.list | Man page |
| logLikBinom.add.reparam.general | Source code |
| logLikBinom.indep | Source code |
| logLikBinom.indep.add.reparam3.general | Source code |
| logistic | Source code |
| logistic.dsgnMat | Source code |
| logistic.vnames | Source code |
| logit | Source code |
| loglikeAndRank | Source code |
| makeBetaTable.general | Source code |
| makeCI.nice | Source code |
| makeVector | Source code |
| match.order | Source code Source code Source code |
| matchNames | Source code |
| matrix2rda | Source code |
| matrixDivideVec | Source code |
| matrixMultVec | Source code |
| mergeData | Source code |
| mergePhenoGeno | Source code |
| meta.EB | Source code |
| meta.GxE | Source code |
| meta.fixed | Source code |
| multiGrep | Source code Source code |
| myAR.E | Source code |
| myAR.E2 | Source code |
| myAR.G | Source code |
| myAR.G2 | Source code |
| myCbind | Source code |
| myConvertLevel | Source code Source code |
| myDummyVar | Source code |
| myDummyVar3 | Source code Source code |
| myExpectedGenotype2 | Source code |
| myInteractMatrix2 | Source code Source code |
| myInterval | Source code |
| myMatrixPlot | Source code |
| myOR.CI3 | Source code Source code |
| myPasteCols | Source code |
| myPercent | Source code Source code |
| myPlot_OR_E | Source code |
| myPlot_genScoreCompare | Source code |
| myProcess.myStrat.inter.OR.CI4 | Source code |
| mySnp.logistic2 | Source code |
| myStrat.inter.OR.CI4 | Source code |
| myStratOR.big | Source code |
| myStrataVar | Source code |
| mylog | Source code |
| mylog2 | Source code |
| myprintVars | Source code |
| myrmvnorm | Source code |
| nnmatch | Source code |
| normVarNames | Source code |
| nsnps.genoFile | Source code |
| orderSNP | Source code |
| orderVars | Source code |
| outNames.cov | Source code |
| outNames.cov2 | Source code |
| outNames.me | Source code |
| pair.match | Source code |
| parse.vec | Source code |
| parseDelimVec | Source code |
| partialDeriv.P.betas | Source code |
| pheno.addFormula | Source code |
| pheno.list | Man page |
| pheno.removeMiss | Source code |
| pipe.genoFile.GLU | Source code |
| populPrev | Source code |
| populPrev2 | Source code |
| possibleComb | Source code Source code |
| postEps.small | Source code |
| powerCount | Source code |
| print.additive.test | Source code |
| print.score.test | Source code |
| print.score.wald | Source code |
| print.snp.effects | Source code |
| print.snp.effects.method | Source code |
| print.snp.logistic | Source code |
| print.snp.matched | Source code |
| printEffects | Man page Source code |
| probit.retro | Source code |
| pvalue.normal | Source code |
| rank.trunc.prod | Source code |
| readFile.gz2 | Source code |
| readFile.gzip3 | Source code |
| readFile.type2 | Source code |
| readFile.zip2 | Source code |
| readTable | Source code |
| read_C_GZ_file | Source code |
| read_tped | Source code |
| recode.geno | Source code |
| removeLeading0 | Source code |
| removeMiss | Source code |
| removeMiss.vars | Source code |
| removeOrKeepCols | Source code |
| removeOrKeepRows | Source code |
| removeWhiteSpace | Source code |
| renameVar | Source code |
| rep.cols | Source code |
| rep.mat | Source code |
| rep.rows | Source code |
| replaceStr.list | Source code |
| replaceStr.var | Source code |
| riskAdd_LT | Source code |
| riskAdd_LT2 | Source code |
| riskAdd_LT3 | Source code |
| riskAdd_LT_general | Source code |
| ro.th.small4.indep.tmp | Source code |
| ro.th.small4.indep2 | Source code |
| ro.th.small4.tmp | Source code |
| sMatrix.logistic | Source code |
| save.plot | Source code |
| scan.UML_CML | Source code |
| scan.change.tab | Source code |
| scan.check.transform | Source code |
| scan.coxph | Source code |
| scan.error | Source code |
| scan.file | Source code |
| scan.include.snps | Source code |
| scan.lin_log | Source code |
| scan.linear | Source code |
| scan.logistic | Source code |
| scan.stream | Source code |
| scanFile | Source code |
| scanNextObs | Source code |
| score.logReg | Source code |
| score.test | Source code |
| score.wald | Source code |
| scoreTest.general9 | Source code |
| scoreTest.small.logit5.max | Source code |
| scoreTest.small.logit5.max.indep6 | Source code |
| set.plot | Source code |
| setDevice | Source code |
| setLists | Source code |
| setPhenoList | Source code |
| setUp.snp.list.stream | Source code |
| setUp.stream | Source code |
| setUpSummary | Source code |
| setup.coxph | Source code |
| setup.lin_log | Source code |
| setup.linear | Source code |
| setup.logistic | Source code |
| snp.ccl.main | Source code |
| snp.delete.files | Source code |
| snp.effects | Man page Source code |
| snp.effects.plot | Man page Source code |
| snp.hcl.main | Source code |
| snp.list | Man page |
| snp.logistic | Man page Source code |
| snp.main | Source code |
| snp.matched | Man page |
| snp.scan.logistic | Source code |
| snp.score | Man page Source code |
| snpPlot3 | Source code |
| snps.genoFile.GLU | Source code |
| sort2D | Source code |
| standardize.z | Source code |
| strCombine2 | Source code Source code |
| strataMatrix | Source code |
| subject.list | Man page |
| subs.genoFile.GLU | Source code |
| subsetData.list | Source code |
| subsetData.var | Source code |
| summary.snp.logistic | Source code |
| summary.snp.matched | Source code |
| swap2cols.cov | Source code |
| table2Format | Source code |
| threshold.trunc.prod | Source code |
| transCall.genoFile.GLU | Source code |
| transform.genoFile | Source code |
| transform.genoFile.GLU | Source code |
| transform.genoFile.PLINK | Source code |
| transform.loc | Source code |
| unadjustedGLM.counts | Source code |
| unfactor | Source code |
| unfactor.all | Source code |
| update.snp.list | Source code |
| update.snpNames | Source code |
| variablePrep2 | Source code |
| variablePrep3 | Source code |
| wald.weight.indep | Source code |
| waldTest.main | Source code |
| writeOut | Source code |
| writeSnpLines | Source code |
| writeTable | Source code |
| writeVec | Source code |
| writeVecToFile | Source code |
