| .onLoad |
Source code
|
| CrossInfo |
Man page
|
| CrossInfo-class |
Man page
|
| H5Stack |
Man page
|
| H5Stack-class |
Man page
|
| Package Constants |
Man page
|
| Package Constants-package |
Man page
|
| `$<-.mapping` |
Source code
|
| `[.qtlfeatures` |
Source code
|
| `[.scanonebins` |
Source code
|
| `[<-.mapping` |
Source code
|
| `[[<-.mapping` |
Source code
|
| `names<-.mapping` |
Source code
|
| `otherattributes<-` |
Source code
|
| addXInfo |
Man page
Source code
|
| allKwargs |
Man page
Source code
|
| allNA |
Man page
Source code
|
| allWhite |
Man page
Source code
|
| anyKwargs |
Man page
Source code
|
| as.data.frame.geno |
Man page
Source code
|
| as.data.frame.map |
Man page
Source code
|
| as.data.frame.mapframe |
Man page
Source code
|
| as.data.frame.pheno |
Man page
Source code
|
| as.geno |
Man page
Source code
|
| as.geno.data.frame |
Man page
Source code
|
| as.map |
Man page
Source code
|
| as.map.data.frame |
Man page
Source code
|
| as.map.list |
Man page
Source code
|
| as.map.map |
Man page
Source code
|
| as.map.mapframe |
Man page
Source code
|
| as.map.scanone |
Man page
Source code
|
| as.mapframe |
Man page
Source code
|
| as.mapframe.data.frame |
Man page
Source code
|
| as.mapframe.list |
Man page
Source code
|
| as.mapframe.map |
Man page
Source code
|
| as.mapframe.mapframe |
Man page
Source code
|
| as.mapframe.scanone |
Man page
Source code
|
| as.mapping |
Man page
Source code
|
| as.pheno |
Man page
Source code
|
| as.pheno.data.frame |
Man page
Source code
|
| batchPermScanone |
Man page
Source code
|
| batchPermScanoneF |
Man page
Source code
|
| batchPermScantwo |
Man page
Source code
|
| batchPermScantwoF |
Man page
Source code
|
| batchPhenoScanone |
Man page
Source code
|
| batchPhenoScantwo |
Man page
Source code
|
| batchScan |
Man page
Source code
|
| binLODValues |
Man page
Source code
|
| bstripBlankRows |
Man page
Source code
|
| clamp |
Man page
Source code
|
| closeStack |
Man page
|
| closeStack,H5Stack-method |
Man page
|
| coerceDataFrame |
Man page
Source code
|
| compareCrossInfo |
Man page
|
| compareCrossInfo.cross |
Man page
Source code
|
| compareCrossInfo.geno |
Man page
Source code
|
| compareCrossInfo.pheno |
Man page
Source code
|
| convertMapUnit |
Man page
Source code
|
| copyObjectsHDF5 |
Man page
Source code
|
| crossesEqual |
Man page
Source code
|
| decodeGenotypes |
Man page
Source code
|
| decodeGenotypes.data.frame |
Man page
Source code
|
| decodeGenotypes.integer |
Man page
Source code
|
| decodeGenotypes.matrix |
Man page
Source code
|
| deleteColumn |
Man page
Source code
|
| dispatchFromClassS3 |
Man page
Source code
|
| ellipt |
Man page
Source code
|
| emptyArgs |
Man page
Source code
|
| encodeGenotypes |
Man page
Source code
|
| encodeGenotypes.character |
Man page
Source code
|
| encodeGenotypes.data.frame |
Man page
Source code
|
| encodeGenotypes.matrix |
Man page
Source code
|
| estPhysicalPositions |
Man page
Source code
|
| extractMarkers |
Man page
Source code
|
| extractPseudomarkers |
Man page
Source code
|
| fileID |
Man page
|
| fileID,H5Stack-method |
Man page
|
| findFlanking |
Man page
Source code
|
| findFlanking.map |
Man page
Source code
|
| findFlanking.mapframe |
Man page
Source code
|
| findFlanking.scanone |
Man page
Source code
|
| findFlankingRowIndices |
Man page
Source code
|
| findLoci |
Man page
Source code
|
| findLocusRowIndices |
Man page
Source code
|
| findMarkers |
Man page
Source code
|
| formatChr |
Man page
Source code
|
| formatSeq |
Man page
Source code
|
| genomeOpt |
Man page
Source code
|
| getAlleles |
Man page
|
| getAlleles,CrossInfo-method |
Man page
|
| getAnalysisTitle |
Man page
Source code
|
| getCoercionFromClassS3 |
Man page
Source code
|
| getColIndices |
Man page
Source code
|
| getColMask |
Man page
Source code
|
| getCrosstype |
Man page
|
| getCrosstype,CrossInfo-method |
Man page
|
| getDatColIndices |
Man page
Source code
|
| getFlankingPhenoColIndices |
Man page
Source code
|
| getGenotypes |
Man page
|
| getGenotypes,CrossInfo-method |
Man page
|
| getIdColIndex |
Man page
Source code
|
| getIdColIndex.cross |
Man page
Source code
|
| getIdColIndex.data.frame |
Man page
Source code
|
| getIndices |
Man page
Source code
|
| getIndices.default |
Man page
Source code
|
| getIndices.qtl |
Man page
Source code
|
| getLODMatrix |
Man page
Source code
|
| getLODProfile |
Man page
Source code
|
| getLODProfile.data.frame |
Man page
Source code
|
| getLODProfile.qtl |
Man page
Source code
|
| getLODProfile.scantwo |
Man page
Source code
|
| getLODValues |
Man page
Source code
|
| getLodColIndex |
Man page
Source code
|
| getLodColIndices |
Man page
Source code
|
| getLodColIndices.mapframe |
Man page
Source code
|
| getLodColIndices.scanone |
Man page
Source code
|
| getLodColIndices.scanonebins |
Man page
Source code
|
| getLodColIndices.scanoneperm |
Man page
Source code
|
| getLodColIndices.scantwo |
Man page
Source code
|
| getLodColIndices.scantwoperm |
Man page
Source code
|
| getLodColIndices.summary.scanonebins |
Man page
Source code
|
| getLodColIndices.summary.scanoneperm |
Man page
Source code
|
| getLodColIndices.summary.scantwoperm |
Man page
Source code
|
| getMapNamesHDF5 |
Man page
Source code
|
| getMapSteps |
Man page
Source code
|
| getMapSteps.map |
Man page
Source code
|
| getMapSteps.mapframe |
Man page
Source code
|
| getMapSteps.scanone |
Man page
Source code
|
| getMapUnit |
Man page
Source code
|
| getMapUnit.data.frame |
Man page
Source code
|
| getMapUnit.default |
Man page
Source code
|
| getMapUnit.map |
Man page
Source code
|
| getMapUnit.mapframe |
Man page
Source code
|
| getMapUnit.scanone |
Man page
Source code
|
| getMapUnitSuffix |
Man page
Source code
|
| getMarkerIndices |
Man page
|
| getMarkerIndices,CrossInfo-method |
Man page
|
| getMarkerNames |
Man page
|
| getMarkerNames,CrossInfo-method |
Man page
|
| getMarkerSeqs |
Man page
|
| getMarkerSeqs,CrossInfo-method |
Man page
|
| getMarkers |
Man page
|
| getMarkers,CrossInfo-method |
Man page
|
| getMask |
Man page
Source code
|
| getMetadataCSV |
Man page
Source code
|
| getMissingValueFromClassS3 |
Man page
Source code
|
| getNumMarkers |
Man page
|
| getNumMarkers,CrossInfo-method |
Man page
|
| getNumPhenotypes |
Man page
|
| getNumPhenotypes,CrossInfo-method |
Man page
|
| getNumSamples |
Man page
|
| getNumSamples,CrossInfo-method |
Man page
|
| getNumSeqs |
Man page
|
| getNumSeqs,CrossInfo-method |
Man page
|
| getObjectClassHDF5 |
Man page
Source code
|
| getObjectNamesHDF5 |
Man page
Source code
|
| getPhenoColIndices |
Man page
Source code
|
| getPhenoColIndices.cross |
Man page
Source code
|
| getPhenoColIndices.data.frame |
Man page
Source code
|
| getPhenotypeIndices |
Man page
|
| getPhenotypeIndices,CrossInfo-method |
Man page
|
| getPhenotypeNames |
Man page
|
| getPhenotypeNames,CrossInfo-method |
Man page
|
| getPhenotypes |
Man page
|
| getPhenotypes,CrossInfo-method |
Man page
|
| getPhenotypes.summary.scantwoperm |
Man page
Source code
|
| getPipelineFunction |
Man page
Source code
|
| getPipelineFunctionName |
Man page
Source code
|
| getPipelineName |
Man page
Source code
|
| getPkgAnalysisPipelineNames |
Man page
Source code
|
| getPkgPipelineDocs |
Man page
Source code
|
| getPkgPipelineFunctionNames |
Man page
Source code
|
| getPkgPipelineInfo |
Man page
Source code
|
| getPkgPipelineNames |
Man page
Source code
|
| getPkgPipelineUsage |
Man page
Source code
|
| getPosColDataMapUnit |
Man page
Source code
|
| getPosColDataMapUnit.character |
Man page
Source code
|
| getPosColDataMapUnit.data.frame |
Man page
Source code
|
| getPosColDataMapUnit.numeric |
Man page
Source code
|
| getPosColIndex |
Man page
Source code
|
| getPosColNameMapUnit |
Man page
Source code
|
| getPosColNameMapUnit.character |
Man page
Source code
|
| getPosColNameMapUnit.data.frame |
Man page
Source code
|
| getQTLFeatures |
Man page
Source code
|
| getQTLIntervals |
Man page
Source code
|
| getQTLIntervals.mapframe |
Man page
Source code
|
| getQTLIntervals.qtl |
Man page
Source code
|
| getQTLIntervals.scanone |
Man page
Source code
|
| getQTLPeaks |
Man page
Source code
|
| getQTLPeaks.mapframe |
Man page
Source code
|
| getQTLPeaks.qtl |
Man page
Source code
|
| getQTLPeaks.scanone |
Man page
Source code
|
| getResultAnalysesHDF5 |
Man page
Source code
|
| getResultInfoHDF5 |
Man page
Source code
|
| getResultNamesHDF5 |
Man page
Source code
|
| getResultPhenotypesHDF5 |
Man page
Source code
|
| getRowIndices |
Man page
Source code
|
| getRowMask |
Man page
Source code
|
| getRunIndexList |
Man page
Source code
|
| getRunIndices |
Man page
Source code
|
| getSampleIndices |
Man page
|
| getSampleIndices,CrossInfo-method |
Man page
|
| getSampleNames |
Man page
|
| getSampleNames,CrossInfo-method |
Man page
|
| getSamples |
Man page
|
| getSamples,CrossInfo-method |
Man page
|
| getSamplesVCF |
Man page
Source code
|
| getScanoneThresholdInfo |
Man page
Source code
|
| getScanoneThresholdInfo.numeric |
Man page
Source code
|
| getScanoneThresholdInfo.qtlintervals |
Man page
Source code
|
| getScanoneThresholdInfo.summary.scanonebins |
Man page
Source code
|
| getScanoneThresholdInfo.summary.scanoneperm |
Man page
Source code
|
| getSeqColIndex |
Man page
Source code
|
| getSeqIndices |
Man page
|
| getSeqIndices,CrossInfo-method |
Man page
|
| getSeqMarkers |
Man page
|
| getSeqMarkers,CrossInfo-method |
Man page
|
| getSeqNames |
Man page
|
| getSeqNames,CrossInfo-method |
Man page
|
| getSeqTable |
Man page
Source code
|
| getSeqinfo |
Man page
Source code
|
| getSequences |
Man page
|
| getSequences,CrossInfo-method |
Man page
|
| getSpecialAttributeNames |
Man page
Source code
|
| getStrainIndices |
Man page
|
| getStrainIndices,CrossInfo-method |
Man page
|
| getTetradIndices |
Man page
|
| getTetradIndices,CrossInfo-method |
Man page
|
| getXInfoFromFilenames |
Man page
Source code
|
| gmapframe |
Man page
Source code
|
| h5writeAttributes |
Man page
Source code
|
| hasCrossHDF5 |
Man page
Source code
|
| hasEnumGenotypes |
Man page
Source code
|
| hasFounderGenotypes |
Man page
Source code
|
| hasGenoQualVCF |
Man page
Source code
|
| hasMapCSV |
Man page
Source code
|
| hasMapHDF5 |
Man page
Source code
|
| hasMarkerSeqs |
Man page
|
| hasMarkerSeqs,CrossInfo-method |
Man page
|
| hasNames |
Man page
Source code
|
| hasObjectHDF5 |
Man page
Source code
|
| hasPhysicalPositions |
Man page
Source code
|
| hasResultsOverviewHDF5 |
Man page
Source code
|
| hasRownames |
Man page
Source code
|
| hasSampleIDs |
Man page
|
| hasSampleIDs,CrossInfo-method |
Man page
|
| hasStrainIndices |
Man page
|
| hasStrainIndices,CrossInfo-method |
Man page
|
| hasTetradIndices |
Man page
|
| hasTetradIndices,CrossInfo-method |
Man page
|
| hasTimeSeriesPhenotypes |
Man page
Source code
|
| inMapOrder |
Man page
Source code
|
| inMapOrder.data.frame |
Man page
Source code
|
| inMapOrder.map |
Man page
Source code
|
| inRange |
Man page
Source code
|
| inferFormatFromFilename |
Man page
Source code
|
| inferLodColNames |
Man page
Source code
|
| inferMapStep |
Man page
Source code
|
| inferStepSize |
Man page
Source code
|
| inferStrainIndices |
Man page
|
| inferStrainIndices.character |
Man page
Source code
|
| inferStrainIndices.cross |
Man page
Source code
|
| inferTetradIndices |
Man page
Source code
|
| inferTetradIndices.character |
Man page
Source code
|
| inferTetradIndices.cross |
Man page
Source code
|
| inferTimeStep |
Man page
Source code
|
| initialize |
Man page
|
| initialize,H5Stack-method |
Man page
|
| insertColumn |
Man page
Source code
|
| interpTimeSeries |
Man page
Source code
|
| intersectLoci |
Man page
Source code
|
| is.mapping |
Man page
Source code
|
| isBOOL |
Man page
Source code
|
| isDefaultMarkerID |
Man page
Source code
|
| isDefaultQTLName |
Man page
Source code
|
| isEnumAllele |
Man page
Source code
|
| isEnumGenotype |
Man page
Source code
|
| isFALSE |
Man page
Source code
|
| isFounderAllele |
Man page
Source code
|
| isFounderGenotype |
Man page
Source code
|
| isGeneticMap |
Man page
Source code
|
| isGeneticMapUnit |
Man page
Source code
|
| isGeneticMapframe |
Man page
Source code
|
| isMarkerID |
Man page
Source code
|
| isNegativeNumber |
Man page
Source code
|
| isNonNegativeNumber |
Man page
Source code
|
| isNormChr |
Man page
Source code
|
| isNormSeq |
Man page
Source code
|
| isPhysicalMap |
Man page
Source code
|
| isPhysicalMapUnit |
Man page
Source code
|
| isPhysicalMapframe |
Man page
Source code
|
| isPositiveNumber |
Man page
Source code
|
| isPositiveWholeNumber |
Man page
Source code
|
| isProbability |
Man page
Source code
|
| isPseudomarkerID |
Man page
Source code
|
| isRawAllele |
Man page
Source code
|
| isRawGenotype |
Man page
Source code
|
| isSingleChar |
Man page
Source code
|
| isSingleFiniteNumber |
Man page
Source code
|
| isSingleNonNegativeNumber |
Man page
Source code
|
| isSingleNonNegativeWholeNumber |
Man page
Source code
|
| isSinglePositiveNumber |
Man page
Source code
|
| isSinglePositiveWholeNumber |
Man page
Source code
|
| isSingleProbability |
Man page
Source code
|
| isSingleString |
Man page
Source code
|
| isSingleWholeNumber |
Man page
Source code
|
| isValidAllele |
Man page
Source code
|
| isValidGenotype |
Man page
Source code
|
| isValidID |
Man page
Source code
|
| isValidMapUnit |
Man page
Source code
|
| isValidName |
Man page
Source code
|
| isWholeNumber |
Man page
Source code
|
| joinH5ObjectNameParts |
Man page
Source code
|
| joinSeqLabels |
Man page
Source code
|
| length,H5Stack-method |
Man page
|
| listGenomes |
Man page
Source code
|
| listWorksheets |
Man page
Source code
|
| loadChrTable |
Man page
Source code
|
| loadMapping |
Man page
Source code
|
| loadSeqTables |
Man page
Source code
|
| loadVector |
Man page
Source code
|
| makeAlleleSet |
Man page
Source code
|
| makeCross |
Man page
Source code
|
| makeDefaultElementNames |
Man page
Source code
|
| makeDefaultMapName |
Man page
Source code
|
| makeDefaultMarkerIDs |
Man page
Source code
|
| makeDefaultQTLNames |
Man page
Source code
|
| makeEnumGenoMatrix |
Man page
Source code
|
| makeFounderGenoMatrix |
Man page
Source code
|
| makeGeno |
Man page
Source code
|
| makeGenotypeSet |
Man page
Source code
|
| makeGroupObjectNames |
Man page
Source code
|
| makeLODBinLabels |
Man page
Source code
|
| makeMapFromDefaultMarkerIDs |
Man page
Source code
|
| makeMapFromDefaultQTLNames |
Man page
Source code
|
| makeMapFromLocusIDs |
Man page
Source code
|
| makeMapFromPseudomarkerIDs |
Man page
Source code
|
| makeNumbers |
Man page
Source code
|
| makePlaceholderMap |
Man page
Source code
|
| makePlaceholderPheno |
Man page
Source code
|
| makePseudomarkerIDs |
Man page
Source code
|
| makeResultsOverview |
Man page
Source code
|
| makeScanoneThresholdObject |
Man page
Source code
|
| makeScantwoThresholdObject |
Man page
Source code
|
| makeWorksheetNames |
Man page
Source code
|
| mapframe |
Man page
Source code
|
| mapkey |
Man page
Source code
|
| mapkeyOpt |
Man page
Source code
|
| mapping |
Man page
Source code
|
| mappingKeys |
Man page
Source code
|
| mappingValues |
Man page
Source code
|
| mapsEqual |
Man page
Source code
|
| matchLoci |
Man page
Source code
|
| matchLocusRowIndices |
Man page
Source code
|
| matchSeqRowIndices |
Man page
Source code
|
| mergeLODBinLabels |
Man page
Source code
|
| nodePermScanone |
Man page
Source code
|
| nodePermScanoneF |
Man page
Source code
|
| nodePermScantwo |
Man page
Source code
|
| nodePermScantwoF |
Man page
Source code
|
| nodePhenoScanone |
Man page
Source code
|
| nodePhenoScantwo |
Man page
Source code
|
| normChr |
Man page
Source code
|
| normSeq |
Man page
Source code
|
| normSeq.character |
Man page
Source code
|
| normSeq.data.frame |
Man page
Source code
|
| normSeq.factor |
Man page
Source code
|
| normSeq.integer |
Man page
Source code
|
| normSeq.map |
Man page
Source code
|
| normSeq.numeric |
Man page
Source code
|
| normSeq.scantwo |
Man page
Source code
|
| openStack |
Man page
|
| openStack,H5Stack-method |
Man page
|
| orderChr |
Man page
Source code
|
| orderMap |
Man page
Source code
|
| orderMap.data.frame |
Man page
Source code
|
| orderMap.map |
Man page
Source code
|
| orderSeq |
Man page
Source code
|
| otherattributes |
Man page
Source code
|
| otherattributes<- |
Man page
|
| padBins |
Man page
Source code
|
| padTimeSeries |
Man page
Source code
|
| parseDefaultMarkerIDs |
Man page
Source code
|
| parseDefaultQTLNames |
Man page
Source code
|
| parseFilenames |
Man page
Source code
|
| parseLODBinLabels |
Man page
Source code
|
| parsePseudomarkerIDs |
Man page
Source code
|
| parseWorksheetNames |
Man page
Source code
|
| peek |
Man page
|
| peek,H5Stack-method |
Man page
|
| permCross |
Man page
Source code
|
| permIndices |
Man page
Source code
|
| plotQTLScanone |
Man page
Source code
|
| plotQTLScantwo |
Man page
Source code
|
| plotReportTitlePagePDF |
Man page
Source code
|
| pop |
Man page
|
| pop,H5Stack-method |
Man page
|
| prepPipelineArgparser |
Man page
Source code
|
| print.qtlintervals |
Source code
|
| print.summary.scanonebins |
Man page
Source code
|
| procPipelineArgs |
Man page
Source code
|
| pull.alleles |
Man page
Source code
|
| pull.alleles.cross |
Man page
Source code
|
| pull.alleles.geno |
Man page
Source code
|
| pull.chr |
Man page
Source code
|
| pull.chr.cross |
Man page
Source code
|
| pull.chr.data.frame |
Man page
Source code
|
| pull.chr.geno |
Man page
Source code
|
| pull.chr.list |
Man page
Source code
|
| pull.chr.map |
Man page
Source code
|
| pull.crosstype |
Man page
Source code
|
| pull.crosstype.cross |
Man page
Source code
|
| pull.crosstype.geno |
Man page
Source code
|
| pull.ind |
Man page
Source code
|
| pull.ind.cross |
Man page
Source code
|
| pull.ind.geno |
Man page
Source code
|
| pull.ind.pheno |
Man page
Source code
|
| pullLoci |
Man page
Source code
|
| pullLocusIDs |
Man page
Source code
|
| pullLocusIDs.data.frame |
Man page
Source code
|
| pullLocusIDs.list |
Man page
Source code
|
| pullLocusIDs.map |
Man page
Source code
|
| pullLocusPos |
Man page
Source code
|
| pullLocusPos.data.frame |
Man page
Source code
|
| pullLocusPos.list |
Man page
Source code
|
| pullLocusPos.map |
Man page
Source code
|
| pullLocusPos.mapframe |
Man page
Source code
|
| pullLocusSeq |
Man page
Source code
|
| pullLocusSeq.data.frame |
Man page
Source code
|
| pullLocusSeq.list |
Man page
Source code
|
| pullLocusSeq.map |
Man page
Source code
|
| pullMap |
Man page
Source code
|
| pullMap.cross |
Man page
Source code
|
| pullMap.geno |
Man page
Source code
|
| push |
Man page
|
| push,H5Stack-method |
Man page
|
| pushLoci |
Man page
Source code
|
| pushLocusIDs |
Man page
Source code
|
| pushLocusIDs.data.frame |
Man page
Source code
|
| pushLocusIDs.list |
Man page
Source code
|
| pushLocusIDs.map |
Man page
Source code
|
| pushLocusPos |
Man page
Source code
|
| pushLocusPos.data.frame |
Man page
Source code
|
| pushLocusPos.list |
Man page
Source code
|
| pushLocusPos.map |
Man page
Source code
|
| pushLocusSeq |
Man page
Source code
|
| pushLocusSeq.data.frame |
Man page
Source code
|
| pushLocusSeq.list |
Man page
Source code
|
| pushLocusSeq.map |
Man page
Source code
|
| pushMap |
Man page
Source code
|
| pushMap.geno |
Man page
Source code
|
| qtlintervals |
Man page
Source code
|
| rankChr |
Man page
Source code
|
| rankSeq |
Man page
Source code
|
| readCovarCSV |
Man page
Source code
|
| readCrossCSV |
Man page
Source code
|
| readCrossHDF5 |
Man page
Source code
|
| readDatasetHDF5 |
Man page
Source code
|
| readDatasetHDF5.array |
Man page
Source code
|
| readDatasetHDF5.cross |
Man page
Source code
|
| readDatasetHDF5.data.frame |
Man page
Source code
|
| readDatasetHDF5.default |
Man page
Source code
|
| readDatasetHDF5.list |
Man page
Source code
|
| readDatasetHDF5.map |
Man page
Source code
|
| readDatasetHDF5.mapframe |
Man page
Source code
|
| readDatasetHDF5.matrix |
Man page
Source code
|
| readDatasetHDF5.qtlintervals |
Man page
Source code
|
| readDatasetHDF5.scanone |
Man page
Source code
|
| readDatasetHDF5.scanonebins |
Man page
Source code
|
| readDatasetHDF5.scanoneperm |
Man page
Source code
|
| readDatasetHDF5.scantwo |
Man page
Source code
|
| readDatasetHDF5.scantwoperm |
Man page
Source code
|
| readDatasetHDF5.summary.scanonebins |
Man page
Source code
|
| readDatasetHDF5.summary.scanoneperm |
Man page
Source code
|
| readDatasetHDF5.summary.scantwo |
Man page
Source code
|
| readDatasetHDF5.summary.scantwoperm |
Man page
Source code
|
| readFeaturesGFF |
Man page
Source code
|
| readGenoCSV |
Man page
Source code
|
| readGenoVCF |
Man page
Source code
|
| readMapCSV |
Man page
Source code
|
| readMapHDF5 |
Man page
Source code
|
| readMapframeCSV |
Man page
Source code
|
| readObjectAttributesHDF5 |
Man page
Source code
|
| readPhenoCSV |
Man page
Source code
|
| readResultHDF5 |
Man page
Source code
|
| readResultsOverviewHDF5 |
Man page
Source code
|
| readSnpsVCF |
Man page
Source code
|
| recodeCSV |
Man page
Source code
|
| refreshCross |
Man page
Source code
|
| removeColsNA |
Man page
Source code
|
| removeRowsNA |
Man page
Source code
|
| requestNodes |
Man page
Source code
|
| requestPkgDataPath |
Man page
Source code
|
| resolveAnalysisTitle |
Man page
Source code
|
| resolveH5ObjectName |
Man page
Source code
|
| resolveMapNameHDF5 |
Man page
Source code
|
| resolveScantwoLodtypes |
Man page
Source code
|
| rstripBlankCols |
Man page
Source code
|
| run |
Man page
Source code
|
| run_annoqtl |
Man page
Source code
|
| run_digest |
Man page
Source code
|
| run_estimap |
Man page
Source code
|
| run_interptimes |
Man page
Source code
|
| run_makecross |
Man page
Source code
|
| run_makegeno |
Man page
Source code
|
| run_prep |
Man page
Source code
|
| run_pullmap |
Man page
Source code
|
| run_pushmap |
Man page
Source code
|
| run_recode |
Man page
Source code
|
| run_report |
Man page
Source code
|
| run_scanone |
Man page
Source code
|
| run_scantwo |
Man page
Source code
|
| setAlleles |
Man page
|
| setAlleles,CrossInfo-method |
Man page
|
| setColumnFromRownames |
Man page
Source code
|
| setCrosstype |
Man page
|
| setCrosstype,CrossInfo-method |
Man page
|
| setGenotypes |
Man page
|
| setGenotypes,CrossInfo-method |
Man page
|
| setMapUnit |
Man page
Source code
|
| setMapUnit.data.frame |
Man page
Source code
|
| setMapUnit.list |
Man page
Source code
|
| setMapUnit.map |
Man page
Source code
|
| setMapUnit.mapframe |
Man page
Source code
|
| setMarkerSeqs |
Man page
|
| setMarkerSeqs,CrossInfo-method |
Man page
|
| setMarkers |
Man page
|
| setMarkers,CrossInfo-method |
Man page
|
| setPhenotypes |
Man page
|
| setPhenotypes,CrossInfo-method |
Man page
|
| setPosColDataMapUnit |
Man page
Source code
|
| setPosColDataMapUnit.character |
Man page
Source code
|
| setPosColDataMapUnit.data.frame |
Man page
Source code
|
| setPosColDataMapUnit.numeric |
Man page
Source code
|
| setPosColNameMapUnit |
Man page
Source code
|
| setPosColNameMapUnit.character |
Man page
Source code
|
| setPosColNameMapUnit.data.frame |
Man page
Source code
|
| setRownamesFromColumn |
Man page
Source code
|
| setSamples |
Man page
|
| setSamples,CrossInfo-method |
Man page
|
| setSequences |
Man page
|
| setSequences,CrossInfo-method |
Man page
|
| setStrainIndices |
Man page
|
| setStrainIndices,CrossInfo-method |
Man page
|
| setTetradIndices |
Man page
|
| setTetradIndices,CrossInfo-method |
Man page
|
| setValidity |
Man page
Man page
|
| setValidity,CrossInfo-method |
Man page
|
| setValidity,H5Stack-method |
Man page
|
| setupDefaultMapkeys |
Man page
Source code
|
| shmootl |
Man page
|
| shmootl-package |
Man page
|
| show,H5Stack-method |
Man page
Man page
|
| show.H5Stack |
Man page
Source code
|
| sniffCSV |
Man page
Source code
|
| sortChr |
Man page
Source code
|
| sortSeq |
Man page
Source code
|
| splitH5ObjectName |
Man page
Source code
|
| splitSeqLabels |
Man page
Source code
|
| stopif |
Man page
Source code
|
| stripWhite |
Man page
Source code
|
| subset.summary.scanonebins |
Man page
Source code
|
| subset.summary.scanoneperm |
Man page
Source code
|
| subset.summary.scantwoperm |
Man page
Source code
|
| subsetByLoci |
Man page
Source code
|
| subsetByLoci.map |
Man page
Source code
|
| subsetByLoci.mapframe |
Man page
Source code
|
| subsetByLocusID |
Man page
Source code
|
| subsetByLocusID.data.frame |
Man page
Source code
|
| subsetByLocusID.map |
Man page
Source code
|
| subsetBySeq |
Man page
Source code
|
| subsetBySeq.character |
Man page
Source code
|
| subsetBySeq.data.frame |
Man page
Source code
|
| subsetBySeq.map |
Man page
Source code
|
| subsetBySeq.qtlintervals |
Man page
Source code
|
| subsetBySeq.scantwo |
Man page
Source code
|
| subsetMap |
Man page
Source code
|
| summary,H5Stack-method |
Man page
|
| summary.H5Stack |
Man page
Source code
|
| summary.scanonebins |
Man page
Source code
|
| testQTLPeakSignificance |
Man page
Source code
|
| updateResultsOverview |
Man page
Source code
|
| validateAlleleSet |
Man page
Source code
|
| validateAlleles |
Man page
|
| validateAlleles,CrossInfo-method |
Man page
|
| validateCrosstype |
Man page
|
| validateCrosstype,CrossInfo-method |
Man page
|
| validateGeneticMapUnit |
Man page
Source code
|
| validateGenotypeSet |
Man page
Source code
|
| validateGenotypes |
Man page
|
| validateGenotypes,CrossInfo-method |
Man page
|
| validateMap |
Man page
Source code
|
| validateMap.list |
Man page
Source code
|
| validateMap.map |
Man page
Source code
|
| validateMapUnit |
Man page
Source code
|
| validateMapUnit.character |
Man page
Source code
|
| validateMapUnit.default |
Man page
Source code
|
| validateMapframe |
Man page
Source code
|
| validateMapframe.data.frame |
Man page
Source code
|
| validateMapframe.mapframe |
Man page
Source code
|
| validateMapping |
Man page
Source code
|
| validateMarkers |
Man page
|
| validateMarkers,CrossInfo-method |
Man page
|
| validatePhenotypes |
Man page
|
| validatePhenotypes,CrossInfo-method |
Man page
|
| validatePhysicalMapUnit |
Man page
Source code
|
| validateRawGenoArray |
Man page
Source code
|
| validateResultsOverview |
Man page
Source code
|
| validateSamples |
Man page
|
| validateSamples,CrossInfo-method |
Man page
|
| validateSequences |
Man page
|
| validateSequences,CrossInfo-method |
Man page
|
| wasa |
Man page
|
| writeCrossCSV |
Man page
Source code
|
| writeCrossHDF5 |
Man page
Source code
|
| writeDatasetHDF5 |
Man page
Source code
|
| writeDatasetHDF5.array |
Man page
Source code
|
| writeDatasetHDF5.cross |
Man page
Source code
|
| writeDatasetHDF5.data.frame |
Man page
Source code
|
| writeDatasetHDF5.default |
Man page
Source code
|
| writeDatasetHDF5.list |
Man page
Source code
|
| writeDatasetHDF5.map |
Man page
Source code
|
| writeDatasetHDF5.mapframe |
Man page
Source code
|
| writeDatasetHDF5.matrix |
Man page
Source code
|
| writeDatasetHDF5.qtlintervals |
Man page
Source code
|
| writeDatasetHDF5.scanone |
Man page
Source code
|
| writeDatasetHDF5.scanonebins |
Man page
Source code
|
| writeDatasetHDF5.scanoneperm |
Man page
Source code
|
| writeDatasetHDF5.scantwo |
Man page
Source code
|
| writeDatasetHDF5.scantwoperm |
Man page
Source code
|
| writeDatasetHDF5.summary.scanonebins |
Man page
Source code
|
| writeDatasetHDF5.summary.scanoneperm |
Man page
Source code
|
| writeDatasetHDF5.summary.scantwo |
Man page
Source code
|
| writeDatasetHDF5.summary.scantwoperm |
Man page
Source code
|
| writeDigestExcel |
Man page
Source code
|
| writeGenoCSV |
Man page
Source code
|
| writeMapCSV |
Man page
Source code
|
| writeMapHDF5 |
Man page
Source code
|
| writeMapframeCSV |
Man page
Source code
|
| writeObjectAttributesHDF5 |
Man page
Source code
|
| writePhenoCSV |
Man page
Source code
|
| writeReportExcel |
Man page
Source code
|
| writeReportPDF |
Man page
Source code
|
| writeResultHDF5 |
Man page
Source code
|
| writeResultsOverviewHDF5 |
Man page
Source code
|
| writeWorkbookExcel |
Man page
Source code
|
