Files in gact/shmootl
QTL Analysis Utilities for Yeast
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/CrossInfo-class.R
R/H5Stack-class.R
R/batchScan.R
R/batchScanone.R
R/batchScanoneF.R
R/batchScantwo.R
R/batchScantwoF.R
R/binLODValues.R
R/chr.R
R/compareCrossInfo.R
R/const.R
R/cross.R
R/csv.R
R/decodeGenotypes.R
R/encodeGenotypes.R
R/excel.R
R/geno.R
R/genome.R
R/getLODMatrix.R
R/getLODProfile.R
R/getLODValues.R
R/getQTLFeatures.R
R/getQTLIntervals.R
R/getQTLPeaks.R
R/gff.R
R/hasEnumGenotypes.R
R/hasFounderGenotypes.R
R/hdf5.R
R/map.R
R/mapping.R
R/pdf.R
R/pheno.R
R/pipeline.R
R/plotQTLScanone.R
R/plotQTLScantwo.R
R/qtlfeatures.R
R/qtlintervals.R
R/run.R
R/run_annoqtl.R
R/run_digest.R
R/run_estimap.R
R/run_interptimes.R
R/run_makecross.R
R/run_makegeno.R
R/run_prep.R
R/run_pullmap.R
R/run_pushmap.R
R/run_recode.R
R/run_report.R
R/run_scanone.R
R/run_scantwo.R
R/scanonebins.R
R/seq.R
R/shmootl.R
R/subset.summary.scanoneperm.R
R/subset.summary.scantwoperm.R
R/subsetByLoci.R
R/subsetByLocusID.R
R/subsetBySeq.R
R/util.R
R/vcf.R
R/wasa-data.R
R/zzz.R
README.md
data/wasa.rda
inst/extdata/genomes/SGD_S288C_R64-1-1/seqtab.csv
inst/extdata/genomes/SGD_S288C_R64-2-1/seqtab.csv
inst/extdata/genomes/chrtab.csv
man-roxygen/author-thomas-walsh.R
man-roxygen/author-yue-hu.R
man-roxygen/param-CrossInfo.R
man-roxygen/param-lodcolumn.R
man-roxygen/param-lodcolumns.R
man-roxygen/param-markers.R
man-roxygen/param-n.cluster.R
man-roxygen/param-phenotypes.R
man-roxygen/param-samples.R
man-roxygen/param-sequences.R
man-roxygen/param-strains.R
man-roxygen/param-tetrads.R
man-roxygen/ref-arends-2010.R
man-roxygen/ref-broman-2003.R
man-roxygen/ref-broman-2009.R
man-roxygen/ref-cubillos-2011.R
man-roxygen/ref-kwak-2014.R
man-roxygen/ref-turner-2014.R
man-roxygen/ref-warringer-2008.R
man-roxygen/section-chr-seq.R
man-roxygen/section-default-marker-ids.R
man-roxygen/section-geno-enum.R
man-roxygen/section-geno-founder.R
man-roxygen/section-geno-raw.R
man-roxygen/section-item-ids.R
man-roxygen/section-locus-ids.R
man-roxygen/section-map.R
man-roxygen/section-mapframe.R
man-roxygen/section-mapunits.R
man-roxygen/section-marker-ids.R
man-roxygen/section-permutations.R
man-roxygen/section-phenotype-ids.R
man-roxygen/section-pipelines.R
man-roxygen/section-pseudomarker-ids.R
man-roxygen/section-qtl-names.R
man-roxygen/section-sample-ids.R
man-roxygen/section-syntactic-names.R
man-roxygen/section-tetradic-samples.R
man-roxygen/section-time-series.R
man-roxygen/seealso-rqtl-manual.R
man/CrossInfo-class.Rd
man/H5Stack-class.Rd
man/Package-Constants.Rd
man/addXInfo.Rd
man/allKwargs.Rd
man/allNA.Rd
man/allWhite.Rd
man/anyKwargs.Rd
man/as.data.frame.geno.Rd
man/as.data.frame.map.Rd
man/as.data.frame.mapframe.Rd
man/as.data.frame.pheno.Rd
man/as.geno.Rd
man/as.map.Rd
man/as.mapframe.Rd
man/as.mapping.Rd
man/as.pheno.Rd
man/batchPermScanone.Rd
man/batchPermScanoneF.Rd
man/batchPermScantwo.Rd
man/batchPermScantwoF.Rd
man/batchPhenoScanone.Rd
man/batchPhenoScantwo.Rd
man/batchScan.Rd
man/binLODValues.Rd
man/bstripBlankRows.Rd
man/clamp.Rd
man/closeStack-methods.Rd
man/coerceDataFrame.Rd
man/compareCrossInfo.Rd
man/convertMapUnit.Rd
man/copyObjectsHDF5.Rd
man/crossesEqual.Rd
man/decodeGenotypes.Rd
man/deleteColumn.Rd
man/dispatchFromClassS3.Rd
man/ellipt.Rd
man/emptyArgs.Rd
man/encodeGenotypes.Rd
man/estPhysicalPositions.Rd
man/extractMarkers.Rd
man/extractPseudomarkers.Rd
man/fileID-methods.Rd
man/findFlanking.Rd
man/findFlankingRowIndices.Rd
man/findLoci.Rd
man/findLocusRowIndices.Rd
man/findMarkers.Rd
man/formatChr.Rd
man/formatSeq.Rd
man/genomeOpt.Rd
man/getAlleles-methods.Rd
man/getAnalysisTitle.Rd
man/getCoercionFromClassS3.Rd
man/getColIndices.Rd
man/getColMask.Rd
man/getCrosstype-methods.Rd
man/getDatColIndices.Rd
man/getFlankingPhenoColIndices.Rd
man/getGenotypes-methods.Rd
man/getIdColIndex.Rd
man/getIndices.Rd
man/getLODMatrix.Rd
man/getLODProfile.Rd
man/getLODValues.Rd
man/getLodColIndex.Rd
man/getLodColIndices.Rd
man/getMapNamesHDF5.Rd
man/getMapSteps.Rd
man/getMapUnit.Rd
man/getMapUnitSuffix.Rd
man/getMarkerIndices-methods.Rd
man/getMarkerNames-methods.Rd
man/getMarkerSeqs-methods.Rd
man/getMarkers-methods.Rd
man/getMask.Rd
man/getMetadataCSV.Rd
man/getMissingValueFromClassS3.Rd
man/getNumMarkers-methods.Rd
man/getNumPhenotypes-methods.Rd
man/getNumSamples-methods.Rd
man/getNumSeqs-methods.Rd
man/getObjectClassHDF5.Rd
man/getObjectNamesHDF5.Rd
man/getPhenoColIndices.Rd
man/getPhenotypeIndices-methods.Rd
man/getPhenotypeNames-methods.Rd
man/getPhenotypes-methods.Rd
man/getPhenotypes.summary.scantwoperm.Rd
man/getPipelineFunction.Rd
man/getPipelineFunctionName.Rd
man/getPipelineName.Rd
man/getPkgAnalysisPipelineNames.Rd
man/getPkgPipelineDocs.Rd
man/getPkgPipelineFunctionNames.Rd
man/getPkgPipelineInfo.Rd
man/getPkgPipelineNames.Rd
man/getPkgPipelineUsage.Rd
man/getPosColDataMapUnit.Rd
man/getPosColIndex.Rd
man/getPosColNameMapUnit.Rd
man/getQTLFeatures.Rd
man/getQTLIntervals.Rd
man/getQTLPeaks.Rd
man/getResultAnalysesHDF5.Rd
man/getResultInfoHDF5.Rd
man/getResultNamesHDF5.Rd
man/getResultPhenotypesHDF5.Rd
man/getRowIndices.Rd
man/getRowMask.Rd
man/getRunIndexList.Rd
man/getRunIndices.Rd
man/getSampleIndices-methods.Rd
man/getSampleNames-methods.Rd
man/getSamples-methods.Rd
man/getSamplesVCF.Rd
man/getScanoneThresholdInfo.Rd
man/getSeqColIndex.Rd
man/getSeqIndices-methods.Rd
man/getSeqMarkers-methods.Rd
man/getSeqNames-methods.Rd
man/getSeqTable.Rd
man/getSeqinfo.Rd
man/getSequences-methods.Rd
man/getSpecialAttributeNames.Rd
man/getStrainIndices-methods.Rd
man/getTetradIndices-methods.Rd
man/getXInfoFromFilenames.Rd
man/gmapframe.Rd
man/h5writeAttributes.Rd
man/hasCrossHDF5.Rd
man/hasEnumGenotypes.Rd
man/hasFounderGenotypes.Rd
man/hasGenoQualVCF.Rd
man/hasMapCSV.Rd
man/hasMapHDF5.Rd
man/hasMarkerSeqs-methods.Rd
man/hasNames.Rd
man/hasObjectHDF5.Rd
man/hasPhysicalPositions.Rd
man/hasResultsOverviewHDF5.Rd
man/hasRownames.Rd
man/hasSampleIDs-methods.Rd
man/hasStrainIndices-methods.Rd
man/hasTetradIndices-methods.Rd
man/hasTimeSeriesPhenotypes.Rd
man/inMapOrder.Rd
man/inRange.Rd
man/inferFormatFromFilename.Rd
man/inferLodColNames.Rd
man/inferMapStep.Rd
man/inferStepSize.Rd
man/inferStrainIndices.Rd
man/inferTetradIndices.Rd
man/inferTimeStep.Rd
man/initialize-methods.Rd
man/insertColumn.Rd
man/interpTimeSeries.Rd
man/intersectLoci.Rd
man/is.mapping.Rd
man/isBOOL.Rd
man/isDefaultMarkerID.Rd
man/isDefaultQTLName.Rd
man/isEnumAllele.Rd
man/isEnumGenotype.Rd
man/isFALSE.Rd
man/isFounderAllele.Rd
man/isFounderGenotype.Rd
man/isGeneticMap.Rd
man/isGeneticMapUnit.Rd
man/isGeneticMapframe.Rd
man/isMarkerID.Rd
man/isNegativeNumber.Rd
man/isNonNegativeNumber.Rd
man/isNormChr.Rd
man/isNormSeq.Rd
man/isPhysicalMap.Rd
man/isPhysicalMapUnit.Rd
man/isPhysicalMapframe.Rd
man/isPositiveNumber.Rd
man/isPositiveWholeNumber.Rd
man/isProbability.Rd
man/isPseudomarkerID.Rd
man/isRawAllele.Rd
man/isRawGenotype.Rd
man/isSingleChar.Rd
man/isSingleFiniteNumber.Rd
man/isSingleNonNegativeNumber.Rd
man/isSingleNonNegativeWholeNumber.Rd
man/isSinglePositiveNumber.Rd
man/isSinglePositiveWholeNumber.Rd
man/isSingleProbability.Rd
man/isSingleString.Rd
man/isSingleWholeNumber.Rd
man/isValidAllele.Rd
man/isValidGenotype.Rd
man/isValidID.Rd
man/isValidMapUnit.Rd
man/isValidName.Rd
man/isWholeNumber.Rd
man/joinH5ObjectNameParts.Rd
man/joinSeqLabels.Rd
man/listGenomes.Rd
man/listWorksheets.Rd
man/loadChrTable.Rd
man/loadMapping.Rd
man/loadSeqTables.Rd
man/loadVector.Rd
man/makeAlleleSet.Rd
man/makeCross.Rd
man/makeDefaultElementNames.Rd
man/makeDefaultMapName.Rd
man/makeDefaultMarkerIDs.Rd
man/makeDefaultQTLNames.Rd
man/makeEnumGenoMatrix.Rd
man/makeFounderGenoMatrix.Rd
man/makeGeno.Rd
man/makeGenotypeSet.Rd
man/makeGroupObjectNames.Rd
man/makeLODBinLabels.Rd
man/makeMapFromDefaultMarkerIDs.Rd
man/makeMapFromDefaultQTLNames.Rd
man/makeMapFromLocusIDs.Rd
man/makeMapFromPseudomarkerIDs.Rd
man/makeNumbers.Rd
man/makePlaceholderMap.Rd
man/makePlaceholderPheno.Rd
man/makePseudomarkerIDs.Rd
man/makeResultsOverview.Rd
man/makeScanoneThresholdObject.Rd
man/makeScantwoThresholdObject.Rd
man/makeWorksheetNames.Rd
man/mapframe.Rd
man/mapkey.Rd
man/mapkeyOpt.Rd
man/mapping.Rd
man/mappingKeys.Rd
man/mappingValues.Rd
man/mapsEqual.Rd
man/matchLoci.Rd
man/matchLocusRowIndices.Rd
man/matchSeqRowIndices.Rd
man/mergeLODBinLabels.Rd
man/nodePermScanone.Rd
man/nodePermScanoneF.Rd
man/nodePermScantwo.Rd
man/nodePermScantwoF.Rd
man/nodePhenoScanone.Rd
man/nodePhenoScantwo.Rd
man/normChr.Rd
man/normSeq.Rd
man/openStack-methods.Rd
man/orderChr.Rd
man/orderMap.Rd
man/orderSeq.Rd
man/otherattributes.Rd
man/padBins.Rd
man/padTimeSeries.Rd
man/parseDefaultMarkerIDs.Rd
man/parseDefaultQTLNames.Rd
man/parseFilenames.Rd
man/parseLODBinLabels.Rd
man/parsePseudomarkerIDs.Rd
man/parseWorksheetNames.Rd
man/peek-methods.Rd
man/permCross.Rd
man/permIndices.Rd
man/plotQTLScanone.Rd
man/plotQTLScantwo.Rd
man/plotReportTitlePagePDF.Rd
man/pop-methods.Rd
man/prepPipelineArgparser.Rd
man/print.summary.scanonebins.Rd
man/procPipelineArgs.Rd
man/pull.alleles.Rd
man/pull.chr.Rd
man/pull.crosstype.Rd
man/pull.ind.Rd
man/pullLoci.Rd
man/pullLocusIDs.Rd
man/pullLocusPos.Rd
man/pullLocusSeq.Rd
man/pullMap.Rd
man/push-methods.Rd
man/pushLoci.Rd
man/pushLocusIDs.Rd
man/pushLocusPos.Rd
man/pushLocusSeq.Rd
man/pushMap.Rd
man/qtlintervals.Rd
man/rankChr.Rd
man/rankSeq.Rd
man/readCovarCSV.Rd
man/readCrossCSV.Rd
man/readCrossHDF5.Rd
man/readDatasetHDF5.Rd
man/readFeaturesGFF.Rd
man/readGenoCSV.Rd
man/readGenoVCF.Rd
man/readMapCSV.Rd
man/readMapHDF5.Rd
man/readMapframeCSV.Rd
man/readObjectAttributesHDF5.Rd
man/readPhenoCSV.Rd
man/readResultHDF5.Rd
man/readResultsOverviewHDF5.Rd
man/readSnpsVCF.Rd
man/recodeCSV.Rd
man/refreshCross.Rd
man/removeColsNA.Rd
man/removeRowsNA.Rd
man/requestNodes.Rd
man/requestPkgDataPath.Rd
man/resolveAnalysisTitle.Rd
man/resolveH5ObjectName.Rd
man/resolveMapNameHDF5.Rd
man/resolveScantwoLodtypes.Rd
man/rstripBlankCols.Rd
man/run.Rd
man/run_annoqtl.Rd
man/run_digest.Rd
man/run_estimap.Rd
man/run_interptimes.Rd
man/run_makecross.Rd
man/run_makegeno.Rd
man/run_prep.Rd
man/run_pullmap.Rd
man/run_pushmap.Rd
man/run_recode.Rd
man/run_report.Rd
man/run_scanone.Rd
man/run_scantwo.Rd
man/setAlleles-methods.Rd
man/setColumnFromRownames.Rd
man/setCrosstype-methods.Rd
man/setGenotypes-methods.Rd
man/setMapUnit.Rd
man/setMarkerSeqs-methods.Rd
man/setMarkers-methods.Rd
man/setPhenotypes-methods.Rd
man/setPosColDataMapUnit.Rd
man/setPosColNameMapUnit.Rd
man/setRownamesFromColumn.Rd
man/setSamples-methods.Rd
man/setSequences-methods.Rd
man/setStrainIndices-methods.Rd
man/setTetradIndices-methods.Rd
man/setValidity-methods.Rd
man/setupDefaultMapkeys.Rd
man/shmootl-package.Rd
man/show-methods.Rd
man/sniffCSV.Rd
man/sortChr.Rd
man/sortSeq.Rd
man/splitH5ObjectName.Rd
man/splitSeqLabels.Rd
man/stopif.Rd
man/stripWhite.Rd
man/subset.summary.scanonebins.Rd
man/subset.summary.scanoneperm.Rd
man/subset.summary.scantwoperm.Rd
man/subsetByLoci.Rd
man/subsetByLocusID.Rd
man/subsetBySeq.Rd
man/subsetMap.Rd
man/summary-methods.Rd
man/summary.scanonebins.Rd
man/testQTLPeakSignificance.Rd
man/updateResultsOverview.Rd
man/validateAlleleSet.Rd
man/validateAlleles-methods.Rd
man/validateCrosstype-methods.Rd
man/validateGeneticMapUnit.Rd
man/validateGenotypeSet.Rd
man/validateGenotypes-methods.Rd
man/validateMap.Rd
man/validateMapUnit.Rd
man/validateMapframe.Rd
man/validateMapping.Rd
man/validateMarkers-methods.Rd
man/validatePhenotypes-methods.Rd
man/validatePhysicalMapUnit.Rd
man/validateRawGenoArray.Rd
man/validateResultsOverview.Rd
man/validateSamples-methods.Rd
man/validateSequences-methods.Rd
man/wasa.Rd
man/writeCrossCSV.Rd
man/writeCrossHDF5.Rd
man/writeDatasetHDF5.Rd
man/writeDigestExcel.Rd
man/writeGenoCSV.Rd
man/writeMapCSV.Rd
man/writeMapHDF5.Rd
man/writeMapframeCSV.Rd
man/writeObjectAttributesHDF5.Rd
man/writePhenoCSV.Rd
man/writeReportExcel.Rd
man/writeReportPDF.Rd
man/writeResultHDF5.Rd
man/writeResultsOverviewHDF5.Rd
man/writeWorkbookExcel.Rd
vignettes/images/example_lodplot1.png
vignettes/images/example_lodplot2.png
vignettes/images/example_scanfile.png
vignettes/references.bib
vignettes/shmootl-devnotes.Rmd
vignettes/shmootl-guide.Rmd
