API for ARTP
Gene and Pathway p-Values Computed using the Adaptive Rank Truncated Product
| Global functions | |
|---|---|
| ARTP | Man page |
| ARTP_pathway | Man page Source code |
| GC.adj.pvalues | Source code |
| LOR.flip | Source code |
| OR.getTitle | Source code |
| OR.plot.main | Source code |
| OR.plot.type | Source code |
| OR.plot.type.method | Source code |
| QQ.plot | Source code |
| QQ.plot2 | Source code |
| SAS2Format | Source code |
| addColumn | Source code |
| addInterVars | Source code |
| addIntercept | Source code |
| addLineSegments | Source code |
| addMissingSNPs | Source code |
| allele.flip | Source code |
| appendFiles | Source code |
| applyFormulas | Source code |
| blockDiag | Source code |
| cal.expect | Source code |
| callGLM | Source code |
| callOS | Source code |
| changeAlleles | Source code |
| changeGenotypes | Source code |
| changeLevels.var | Source code |
| changeStr.names | Source code |
| changeStrata | Source code |
| check.data.list | Source code |
| check.file.list | Source code |
| check.files | Source code |
| check.gene.list | Source code |
| check.group.list | Source code |
| check.list.vec.char | Source code |
| check.locusMap.list | Source code |
| check.obs.list | Source code |
| check.perm.list | Source code |
| check.pheno.list | Source code |
| check.snp.list | Source code |
| check.study.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 |
| checkDelimiter | Source code |
| checkForConstantVar | Source code |
| checkForSep | 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 |
| chromosome.plot | Source code |
| closeFile | Source code |
| combObserved.study | Source code |
| combPerm.study | Source code |
| combPvalue.log | Source code |
| combVars.study | Source code |
| combineByPathway_Kai | Source code |
| combineTime | Source code |
| convert.obsfile | 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 |
| effects.init | Source code |
| exportSAS | Source code |
| extractByStr | Source code |
| factorVars | Source code |
| freqCounts.var | Source code |
| gene.getOrder | Source code |
| gene.list | Man page |
| gene.plot | Source code |
| gene.plot.colors | Source code |
| gene.plot.main | Source code |
| gene.transform.loc | Source code |
| geneSNPs.study | Source code |
| geneStat.obs | Source code |
| geneStat.perm | Source code |
| geneStats.init | Source code |
| gene_SNP_data | Man page |
| genfile.list | Source code |
| genfile.vec | Source code |
| geno_data | Man page |
| get.in.miss | Source code |
| getAllVars | Source code |
| getCI | Source code |
| getColNumber | Source code |
| getColors | Source code |
| getColsFromCharVec | Source code |
| getColumns | Source code |
| getCommandArg | Source code |
| getData.1 | Source code |
| getDelimiter | Source code |
| getDesignMatrix | Source code |
| getEstCov | Source code |
| getExtremeSubs | Source code |
| getFID | Source code |
| getFID.study | Source code |
| getFileDelim | Source code |
| getFileHeader | Source code |
| getFileType | Source code |
| getFormulas | Source code |
| getGene.parms | Source code |
| getGenoCounts | Source code |
| getGenoStats | Source code |
| getIdsFromFile | Source code |
| getInheritanceVec | Source code |
| getInteractions | Source code |
| getLinearComb.var | Source code |
| getListName | Source code |
| getLocusMap | Source code |
| getLoglike.glm | Source code |
| getMAF | Source code |
| getMAF.control | Source code |
| getMinPerm.study | Source code |
| getModelData | Source code |
| getNames | Source code |
| getNcols | Source code |
| getNcols.study | Source code |
| getNextObs | Source code |
| getNperm | Source code |
| getNperm.study | Source code |
| getNrows | Source code |
| getOR.CI | Source code |
| getORfromLOR | Source code |
| getObserved.study | Source code |
| getObserved.vec | Source code |
| getOrder | Source code |
| getPermutation | Source code |
| getPermutation.strata | Source code |
| getPheno.info | Source code |
| getPhenoData | Source code |
| getRead.n | Source code |
| getReadN.double | Source code |
| getRow1.omitN | Source code |
| getSASData | Source code |
| getSNPnames.study | Source code |
| getSnpLoadList | Source code |
| getSnpNames | Source code |
| getSubjIds | Source code |
| getSubject.vec | Source code |
| getSubsetDataVars | Source code |
| getSummary | Source code |
| getSummary.main | Source code |
| getTempfile | Source code |
| getUniqueChrm | Source code |
| getUniqueVarName | Source code |
| getVarNames | Source code |
| getVarNames.int | Source code |
| getVarNames.snp | Source code |
| getVecFromStr | Source code |
| getWaldTest | Source code |
| getXBeta | Source code |
| globalAlleles | Source code |
| glu.SNP_bins | Source code |
| glu.commonSNPs | Source code |
| glu.create_ped | 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 |
| heterTest | Source code |
| inflationFactor | 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 |
| loglikeAndRank | Source code |
| makeVector | Source code |
| matchNames | Source code |
| matrix2rda | Source code |
| matrixDivideVec | Source code |
| matrixMultVec | Source code |
| mergeData | Source code |
| mergePhenoGeno | Source code |
| meta | Source code |
| meta.analysis | Source code |
| meta.mima.scan | Source code |
| meta.setup | Source code |
| meta.update | Source code |
| mima | Source code |
| myrmvnorm | Source code |
| normVarNames | Source code |
| obs_pvalues | Man page |
| orderSNP | Source code |
| orderVars | Source code |
| parse.vec | Source code |
| perm.closeFiles | Source code |
| perm.deleteFiles | Source code |
| perm.getData | Source code |
| perm.glm | Source code |
| perm.openFiles | Source code |
| perm.readData | Source code |
| permReg | Source code |
| perm_pvalues | Man page |
| pheno.list | Man page |
| pheno_data | Man page |
| plot_genes | Man page 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 |
| readPermData | Source code |
| readTable | 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 |
| runPermutations | Man page Source code |
| save.plot | Source code |
| scanFile | Source code |
| scanNextObs | Source code |
| score.logReg | Source code |
| set.plot | Source code |
| setDevice | Source code |
| setUp.stream | Source code |
| setUpSummary | Source code |
| single.marker.test | Man page Source code |
| snp.effects | Source code |
| snp.effects.plot | Source code |
| snp.list | Man page |
| sort2D | Source code |
| standardize.z | Source code |
| strataMatrix | Source code |
| subsetData.list | Source code |
| subsetData.var | Source code |
| subsetPermData | Source code |
| swap2cols.cov | Source code |
| table2Format | Source code |
| threshold.trunc.prod | 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 |
| waldTest.main | Source code |
| writeSnpLines | Source code |
| writeTable | Source code |
| writeVec | Source code |
| writeVecToFile | Source code |
