API for gact/shmootl
QTL Analysis Utilities for Yeast

Global functions
CrossInfo Man page
CrossInfo-class Man page
H5Stack Man page
H5Stack-class Man page
Package Constants Man page
Package Constants-package Man page
addXInfo Man page
allKwargs Man page
allNA Man page
allWhite Man page
anyKwargs Man page
as.data.frame.geno Man page
as.data.frame.map Man page
as.data.frame.mapframe Man page
as.data.frame.pheno Man page
as.geno Man page
as.geno.data.frame Man page
as.map Man page
as.map.data.frame Man page
as.map.list Man page
as.map.map Man page
as.map.mapframe Man page
as.map.scanone Man page
as.mapframe Man page
as.mapframe.data.frame Man page
as.mapframe.list Man page
as.mapframe.map Man page
as.mapframe.mapframe Man page
as.mapframe.scanone Man page
as.mapping Man page
as.pheno Man page
as.pheno.data.frame Man page
batchPermScanone Man page
batchPermScanoneF Man page
batchPermScantwo Man page
batchPermScantwoF Man page
batchPhenoScanone Man page
batchPhenoScantwo Man page
batchScan Man page
binLODValues Man page
bstripBlankRows Man page
clamp Man page
closeStack Man page
closeStack,H5Stack-method Man page
coerceDataFrame Man page
compareCrossInfo Man page
compareCrossInfo.cross Man page
compareCrossInfo.geno Man page
compareCrossInfo.pheno Man page
convertMapUnit Man page
copyObjectsHDF5 Man page
crossesEqual Man page
decodeGenotypes Man page
decodeGenotypes.data.frame Man page
decodeGenotypes.integer Man page
decodeGenotypes.matrix Man page
deleteColumn Man page
dispatchFromClassS3 Man page
ellipt Man page
emptyArgs Man page
encodeGenotypes Man page
encodeGenotypes.character Man page
encodeGenotypes.data.frame Man page
encodeGenotypes.matrix Man page
estPhysicalPositions Man page
extractMarkers Man page
extractPseudomarkers Man page
fileID Man page
fileID,H5Stack-method Man page
findFlanking Man page
findFlanking.map Man page
findFlanking.mapframe Man page
findFlanking.scanone Man page
findFlankingRowIndices Man page
findLoci Man page
findLocusRowIndices Man page
findMarkers Man page
formatChr Man page
formatSeq Man page
genomeOpt Man page
getAlleles Man page
getAlleles,CrossInfo-method Man page
getAnalysisTitle Man page
getCoercionFromClassS3 Man page
getColIndices Man page
getColMask Man page
getCrosstype Man page
getCrosstype,CrossInfo-method Man page
getDatColIndices Man page
getFlankingPhenoColIndices Man page
getGenotypes Man page
getGenotypes,CrossInfo-method Man page
getIdColIndex Man page
getIdColIndex.cross Man page
getIdColIndex.data.frame Man page
getIndices Man page
getIndices.default Man page
getIndices.qtl Man page
getLODMatrix Man page
getLODProfile Man page
getLODProfile.data.frame Man page
getLODProfile.qtl Man page
getLODProfile.scantwo Man page
getLODValues Man page
getLodColIndex Man page
getLodColIndices Man page
getLodColIndices.mapframe Man page
getLodColIndices.scanone Man page
getLodColIndices.scanonebins Man page
getLodColIndices.scanoneperm Man page
getLodColIndices.scantwo Man page
getLodColIndices.scantwoperm Man page
getLodColIndices.summary.scanonebins Man page
getLodColIndices.summary.scanoneperm Man page
getLodColIndices.summary.scantwoperm Man page
getMapNamesHDF5 Man page
getMapSteps Man page
getMapSteps.map Man page
getMapSteps.mapframe Man page
getMapSteps.scanone Man page
getMapUnit Man page
getMapUnit.data.frame Man page
getMapUnit.default Man page
getMapUnit.map Man page
getMapUnit.mapframe Man page
getMapUnit.scanone Man page
getMapUnitSuffix Man page
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
getMetadataCSV Man page
getMissingValueFromClassS3 Man page
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
getObjectNamesHDF5 Man page
getPhenoColIndices Man page
getPhenoColIndices.cross Man page
getPhenoColIndices.data.frame Man page
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
getPipelineFunction Man page
getPipelineFunctionName Man page
getPipelineName Man page
getPkgAnalysisPipelineNames Man page
getPkgPipelineDocs Man page
getPkgPipelineFunctionNames Man page
getPkgPipelineInfo Man page
getPkgPipelineNames Man page
getPkgPipelineUsage Man page
getPosColDataMapUnit Man page
getPosColDataMapUnit.character Man page
getPosColDataMapUnit.data.frame Man page
getPosColDataMapUnit.numeric Man page
getPosColIndex Man page
getPosColNameMapUnit Man page
getPosColNameMapUnit.character Man page
getPosColNameMapUnit.data.frame Man page
getQTLFeatures Man page
getQTLIntervals Man page
getQTLIntervals.mapframe Man page
getQTLIntervals.qtl Man page
getQTLIntervals.scanone Man page
getQTLPeaks Man page
getQTLPeaks.mapframe Man page
getQTLPeaks.qtl Man page
getQTLPeaks.scanone Man page
getResultAnalysesHDF5 Man page
getResultInfoHDF5 Man page
getResultNamesHDF5 Man page
getResultPhenotypesHDF5 Man page
getRowIndices Man page
getRowMask Man page
getRunIndexList Man page
getRunIndices Man page
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
getScanoneThresholdInfo Man page
getScanoneThresholdInfo.numeric Man page
getScanoneThresholdInfo.qtlintervals Man page
getScanoneThresholdInfo.summary.scanonebins Man page
getScanoneThresholdInfo.summary.scanoneperm Man page
getSeqColIndex Man page
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
getSeqinfo Man page
getSequences Man page
getSequences,CrossInfo-method Man page
getSpecialAttributeNames Man page
getStrainIndices Man page
getStrainIndices,CrossInfo-method Man page
getTetradIndices Man page
getTetradIndices,CrossInfo-method Man page
getXInfoFromFilenames Man page
gmapframe Man page
h5writeAttributes Man page
hasCrossHDF5 Man page
hasEnumGenotypes Man page
hasFounderGenotypes Man page
hasGenoQualVCF Man page
hasMapCSV Man page
hasMapHDF5 Man page
hasMarkerSeqs Man page
hasMarkerSeqs,CrossInfo-method Man page
hasNames Man page
hasObjectHDF5 Man page
hasPhysicalPositions Man page
hasResultsOverviewHDF5 Man page
hasRownames Man page
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
inMapOrder Man page
inMapOrder.data.frame Man page
inMapOrder.map Man page
inRange Man page
inferFormatFromFilename Man page
inferLodColNames Man page
inferMapStep Man page
inferStepSize Man page
inferStrainIndices Man page
inferStrainIndices.character Man page
inferStrainIndices.cross Man page
inferTetradIndices Man page
inferTetradIndices.character Man page
inferTetradIndices.cross Man page
inferTimeStep Man page
initialize Man page
initialize,H5Stack-method Man page
insertColumn Man page
interpTimeSeries Man page
intersectLoci Man page
is.mapping Man page
isBOOL Man page
isDefaultMarkerID Man page
isDefaultQTLName Man page
isEnumAllele Man page
isEnumGenotype Man page
isFALSE Man page
isFounderAllele Man page
isFounderGenotype Man page
isGeneticMap Man page
isGeneticMapUnit Man page
isGeneticMapframe Man page
isMarkerID Man page
isNegativeNumber Man page
isNonNegativeNumber Man page
isNormChr Man page
isNormSeq Man page
isPhysicalMap Man page
isPhysicalMapUnit Man page
isPhysicalMapframe Man page
isPositiveNumber Man page
isPositiveWholeNumber Man page
isProbability Man page
isPseudomarkerID Man page
isRawAllele Man page
isRawGenotype Man page
isSingleChar Man page
isSingleFiniteNumber Man page
isSingleNonNegativeNumber Man page
isSingleNonNegativeWholeNumber Man page
isSinglePositiveNumber Man page
isSinglePositiveWholeNumber Man page
isSingleProbability Man page
isSingleString Man page
isSingleWholeNumber Man page
isValidAllele Man page
isValidGenotype Man page
isValidID Man page
isValidMapUnit Man page
isValidName Man page
isWholeNumber Man page
joinH5ObjectNameParts Man page
joinSeqLabels Man page
length,H5Stack-method Man page
listGenomes Man page
listWorksheets Man page
loadChrTable Man page
loadMapping Man page
loadSeqTables Man page
loadVector Man page
makeAlleleSet Man page
makeCross Man page
makeDefaultElementNames Man page
makeDefaultMapName Man page
makeDefaultMarkerIDs Man page
makeDefaultQTLNames Man page
makeEnumGenoMatrix Man page
makeFounderGenoMatrix Man page
makeGeno Man page
makeGenotypeSet Man page
makeGroupObjectNames Man page
makeLODBinLabels Man page
makeMapFromDefaultMarkerIDs Man page
makeMapFromDefaultQTLNames Man page
makeMapFromLocusIDs Man page
makeMapFromPseudomarkerIDs Man page
makeNumbers Man page
makePlaceholderMap Man page
makePlaceholderPheno Man page
makePseudomarkerIDs Man page
makeResultsOverview Man page
makeScanoneThresholdObject Man page
makeScantwoThresholdObject Man page
makeWorksheetNames Man page
mapframe Man page
mapkey Man page
mapkeyOpt Man page
mapping Man page
mappingKeys Man page
mappingValues Man page
mapsEqual Man page
matchLoci Man page
matchLocusRowIndices Man page
matchSeqRowIndices Man page
mergeLODBinLabels Man page
nodePermScanone Man page
nodePermScanoneF Man page
nodePermScantwo Man page
nodePermScantwoF Man page
nodePhenoScanone Man page
nodePhenoScantwo Man page
normChr Man page
normSeq Man page
normSeq.character Man page
normSeq.data.frame Man page
normSeq.factor Man page
normSeq.integer Man page
normSeq.map Man page
normSeq.numeric Man page
normSeq.scantwo Man page
openStack Man page
openStack,H5Stack-method Man page
orderChr Man page
orderMap Man page
orderMap.data.frame Man page
orderMap.map Man page
orderSeq Man page
otherattributes Man page
otherattributes<- Man page
padBins Man page
padTimeSeries Man page
parseDefaultMarkerIDs Man page
parseDefaultQTLNames Man page
parseFilenames Man page
parseLODBinLabels Man page
parsePseudomarkerIDs Man page
parseWorksheetNames Man page
peek Man page
peek,H5Stack-method Man page
permCross Man page
permIndices Man page
plotQTLScanone Man page
plotQTLScantwo Man page
plotReportTitlePagePDF Man page
pop Man page
pop,H5Stack-method Man page
prepPipelineArgparser Man page
print.summary.scanonebins Man page
procPipelineArgs Man page
pull.alleles Man page
pull.alleles.cross Man page
pull.alleles.geno Man page
pull.chr Man page
pull.chr.cross Man page
pull.chr.data.frame Man page
pull.chr.geno Man page
pull.chr.list Man page
pull.chr.map Man page
pull.crosstype Man page
pull.crosstype.cross Man page
pull.crosstype.geno Man page
pull.ind Man page
pull.ind.cross Man page
pull.ind.geno Man page
pull.ind.pheno Man page
pullLoci Man page
pullLocusIDs Man page
pullLocusIDs.data.frame Man page
pullLocusIDs.list Man page
pullLocusIDs.map Man page
pullLocusPos Man page
pullLocusPos.data.frame Man page
pullLocusPos.list Man page
pullLocusPos.map Man page
pullLocusPos.mapframe Man page
pullLocusSeq Man page
pullLocusSeq.data.frame Man page
pullLocusSeq.list Man page
pullLocusSeq.map Man page
pullMap Man page
pullMap.cross Man page
pullMap.geno Man page
push Man page
push,H5Stack-method Man page
pushLoci Man page
pushLocusIDs Man page
pushLocusIDs.data.frame Man page
pushLocusIDs.list Man page
pushLocusIDs.map Man page
pushLocusPos Man page
pushLocusPos.data.frame Man page
pushLocusPos.list Man page
pushLocusPos.map Man page
pushLocusSeq Man page
pushLocusSeq.data.frame Man page
pushLocusSeq.list Man page
pushLocusSeq.map Man page
pushMap Man page
pushMap.geno Man page
qtlintervals Man page
rankChr Man page
rankSeq Man page
readCovarCSV Man page
readCrossCSV Man page
readCrossHDF5 Man page
readDatasetHDF5 Man page
readDatasetHDF5.array Man page
readDatasetHDF5.cross Man page
readDatasetHDF5.data.frame Man page
readDatasetHDF5.default Man page
readDatasetHDF5.list Man page
readDatasetHDF5.map Man page
readDatasetHDF5.mapframe Man page
readDatasetHDF5.matrix Man page
readDatasetHDF5.qtlintervals Man page
readDatasetHDF5.scanone Man page
readDatasetHDF5.scanonebins Man page
readDatasetHDF5.scanoneperm Man page
readDatasetHDF5.scantwo Man page
readDatasetHDF5.scantwoperm Man page
readDatasetHDF5.summary.scanonebins Man page
readDatasetHDF5.summary.scanoneperm Man page
readDatasetHDF5.summary.scantwo Man page
readDatasetHDF5.summary.scantwoperm Man page
readFeaturesGFF Man page
readGenoCSV Man page
readGenoVCF Man page
readMapCSV Man page
readMapHDF5 Man page
readMapframeCSV Man page
readObjectAttributesHDF5 Man page
readPhenoCSV Man page
readResultHDF5 Man page
readResultsOverviewHDF5 Man page
readSnpsVCF Man page
recodeCSV Man page
refreshCross Man page
removeColsNA Man page
removeRowsNA Man page
requestNodes Man page
requestPkgDataPath Man page
resolveAnalysisTitle Man page
resolveH5ObjectName Man page
resolveMapNameHDF5 Man page
resolveScantwoLodtypes Man page
rstripBlankCols Man page
run Man page
run_annoqtl Man page
run_digest Man page
run_estimap Man page
run_interptimes Man page
run_makecross Man page
run_makegeno Man page
run_prep Man page
run_pullmap Man page
run_pushmap Man page
run_recode Man page
run_report Man page
run_scanone Man page
run_scantwo Man page
setAlleles Man page
setAlleles,CrossInfo-method Man page
setColumnFromRownames Man page
setCrosstype Man page
setCrosstype,CrossInfo-method Man page
setGenotypes Man page
setGenotypes,CrossInfo-method Man page
setMapUnit Man page
setMapUnit.data.frame Man page
setMapUnit.list Man page
setMapUnit.map Man page
setMapUnit.mapframe Man page
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
setPosColDataMapUnit.character Man page
setPosColDataMapUnit.data.frame Man page
setPosColDataMapUnit.numeric Man page
setPosColNameMapUnit Man page
setPosColNameMapUnit.character Man page
setPosColNameMapUnit.data.frame Man page
setRownamesFromColumn Man page
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
shmootl Man page
shmootl-package Man page
show,H5Stack-method Man page Man page
show.H5Stack Man page
sniffCSV Man page
sortChr Man page
sortSeq Man page
splitH5ObjectName Man page
splitSeqLabels Man page
stopif Man page
stripWhite Man page
subset.summary.scanonebins Man page
subset.summary.scanoneperm Man page
subset.summary.scantwoperm Man page
subsetByLoci Man page
subsetByLoci.map Man page
subsetByLoci.mapframe Man page
subsetByLocusID Man page
subsetByLocusID.data.frame Man page
subsetByLocusID.map Man page
subsetBySeq Man page
subsetBySeq.character Man page
subsetBySeq.data.frame Man page
subsetBySeq.map Man page
subsetBySeq.qtlintervals Man page
subsetBySeq.scantwo Man page
subsetMap Man page
summary,H5Stack-method Man page
summary.H5Stack Man page
summary.scanonebins Man page
testQTLPeakSignificance Man page
updateResultsOverview Man page
validateAlleleSet Man page
validateAlleles Man page
validateAlleles,CrossInfo-method Man page
validateCrosstype Man page
validateCrosstype,CrossInfo-method Man page
validateGeneticMapUnit Man page
validateGenotypeSet Man page
validateGenotypes Man page
validateGenotypes,CrossInfo-method Man page
validateMap Man page
validateMap.list Man page
validateMap.map Man page
validateMapUnit Man page
validateMapUnit.character Man page
validateMapUnit.default Man page
validateMapframe Man page
validateMapframe.data.frame Man page
validateMapframe.mapframe Man page
validateMapping Man page
validateMarkers Man page
validateMarkers,CrossInfo-method Man page
validatePhenotypes Man page
validatePhenotypes,CrossInfo-method Man page
validatePhysicalMapUnit Man page
validateRawGenoArray Man page
validateResultsOverview Man page
validateSamples Man page
validateSamples,CrossInfo-method Man page
validateSequences Man page
validateSequences,CrossInfo-method Man page
wasa Man page
writeCrossCSV Man page
writeCrossHDF5 Man page
writeDatasetHDF5 Man page
writeDatasetHDF5.array Man page
writeDatasetHDF5.cross Man page
writeDatasetHDF5.data.frame Man page
writeDatasetHDF5.default Man page
writeDatasetHDF5.list Man page
writeDatasetHDF5.map Man page
writeDatasetHDF5.mapframe Man page
writeDatasetHDF5.matrix Man page
writeDatasetHDF5.qtlintervals Man page
writeDatasetHDF5.scanone Man page
writeDatasetHDF5.scanonebins Man page
writeDatasetHDF5.scanoneperm Man page
writeDatasetHDF5.scantwo Man page
writeDatasetHDF5.scantwoperm Man page
writeDatasetHDF5.summary.scanonebins Man page
writeDatasetHDF5.summary.scanoneperm Man page
writeDatasetHDF5.summary.scantwo Man page
writeDatasetHDF5.summary.scantwoperm Man page
writeDigestExcel Man page
writeGenoCSV Man page
writeMapCSV Man page
writeMapHDF5 Man page
writeMapframeCSV Man page
writeObjectAttributesHDF5 Man page
writePhenoCSV Man page
writeReportExcel Man page
writeReportPDF Man page
writeResultHDF5 Man page
writeResultsOverviewHDF5 Man page
writeWorkbookExcel Man page
gact/shmootl documentation built on June 5, 2019, 10:21 a.m.