Man pages for gact/shmootl
QTL Analysis Utilities for Yeast
| addXInfo | Add experiment info to the given matrix. |
| allKwargs | Test if ellipsis arguments are all keyword arguments. |
| allNA | Test if all elements are 'NA' values. |
| allWhite | Test if vector is all whitespace. |
| anyKwargs | Test if any ellipsis arguments are keyword arguments. |
| as.data.frame.geno | Convert 'geno' object to 'data.frame'. |
| as.data.frame.map | Convert 'map' to 'data.frame'. |
| as.data.frame.mapframe | Convert 'mapframe' to 'data.frame'. |
| as.data.frame.pheno | Convert 'pheno' object to 'data.frame'. |
| as.geno | Convert to 'geno' object. |
| as.map | Convert object to 'map'. |
| as.mapframe | Convert object to 'mapframe'. |
| as.mapping | Convert to a 'mapping' object. |
| as.pheno | Convert to 'pheno' object. |
| batchPermScanone | Run 'qtl::scanone' on a batch of permuted 'cross' objects. |
| batchPermScanoneF | Run 'funqtl::scanoneF' on a batch of permuted 'cross'... |
| batchPermScantwo | Run 'qtl::scantwo' on a batch of permuted 'cross' objects. |
| batchPermScantwoF | Run 'funqtl::scantwoF' on batch of permuted 'cross' objects. |
| batchPhenoScanone | Run 'qtl::scanone' on a batch of phenotypes. |
| batchPhenoScantwo | Run 'qtl::scantwo' on a batch of phenotypes. |
| batchScan | Perform a batch of QTL analysis. |
| binLODValues | Bin LOD values of 'scanone' object. |
| bstripBlankRows | Strip blank rows from bottom of 'data.frame'. |
| clamp | Clamp numbers within a range. |
| closeStack-methods | Close all HDF5 objects in 'H5Stack'. |
| coerceDataFrame | Coerce 'data.frame' columns to the specified classes. |
| compareCrossInfo | Compare object with associated 'CrossInfo'. |
| convertMapUnit | Convert map unit and rescale map positions. |
| copyObjectsHDF5 | Copy objects between HDF5 files. |
| crossesEqual | Test if two 'R/qtl' 'cross' objects are essentially equal. |
| CrossInfo-class | An S4 class to hold yeast cross information. |
| decodeGenotypes | Decode genotype integers to genotype strings. |
| deleteColumn | Delete column from object. |
| dispatchFromClassS3 | Dispatch method with respect to the given class vector. |
| ellipt | Ellipt string to the given length. |
| emptyArgs | Test if ellipsis arguments are empty. |
| encodeGenotypes | Encode genotype strings as genotype integers. |
| estPhysicalPositions | Add estimated physical positions to QTL intervals. |
| extractMarkers | Extract marker loci. |
| extractPseudomarkers | Extract pseudomarker loci. |
| fileID-methods | Get HDF5 object ID of HDF5 file. |
| findFlanking | Find map loci flanking map positions. |
| findFlankingRowIndices | Find row index of flanking 'mapframe' loci. |
| findLoci | Find closest map loci. |
| findLocusRowIndices | Find row index of closest 'mapframe' locus. |
| findMarkers | Find closest markers. |
| formatChr | Format chromosome labels. |
| formatSeq | Format sequence labels. |
| genomeOpt | Set/get genome option. |
| getAlleles-methods | Get allele symbols. |
| getAnalysisTitle | Get analysis title for the given 'shmootl' analysis pipeline. |
| getCoercionFromClassS3 | Get coercion function for the given class. |
| getColIndices | Get column indices of object. |
| getColMask | Get logical mask of object columns. |
| getCrosstype-methods | Get cross type. |
| getDatColIndices | Get data column indices. |
| getFlankingPhenoColIndices | Get flanking phenotype column indices. |
| getGenotypes-methods | Get genotype symbols. |
| getIdColIndex | Get sample ID column index. |
| getIndices | Get indices of object elements. |
| getLodColIndex | Get LOD column index. |
| getLodColIndices | Get LOD column indices. |
| getLODMatrix | Get LOD matrix. |
| getLODProfile | Get LOD profile. |
| getLODValues | Get LOD values. |
| getMapNamesHDF5 | Get names of maps in HDF5 file. |
| getMapSteps | Get steps between loci. |
| getMapUnit | Get map unit. |
| getMapUnitSuffix | Get map unit suffix from a vector of map positions. |
| getMarkerIndices-methods | Get marker indices. |
| getMarkerNames-methods | Get marker names. |
| getMarkerSeqs-methods | Get sequences by marker. |
| getMarkers-methods | Get marker IDs. |
| getMask | Get logical mask of object elements. |
| getMetadataCSV | Get parameters of 'R/qtl' input data. |
| getMissingValueFromClassS3 | Get missing value for the given class. |
| getNumMarkers-methods | Get the number of markers. |
| getNumPhenotypes-methods | Get the number of phenotypes. |
| getNumSamples-methods | Get the number of samples. |
| getNumSeqs-methods | Get the number of sequences. |
| getObjectClassHDF5 | Get R class of a HDF5 object. |
| getObjectNamesHDF5 | Get names of HDF5 objects from HDF5 file and name. |
| getPhenoColIndices | Get phenotype column indices. |
| getPhenotypeIndices-methods | Get phenotype indices. |
| getPhenotypeNames-methods | Get phenotype names. |
| getPhenotypes-methods | Get phenotype IDs. |
| getPhenotypes.summary.scantwoperm | Get phenotype names. |
| getPipelineFunction | Get 'shmootl' pipeline function. |
| getPipelineFunctionName | Get function name for the given 'shmootl' pipeline. |
| getPipelineName | Get 'shmootl' pipeline name for the given function. |
| getPkgAnalysisPipelineNames | Get 'shmootl' analysis pipeline names. |
| getPkgPipelineDocs | Get 'shmootl' pipeline docs. |
| getPkgPipelineFunctionNames | Get 'shmootl' pipeline function names. |
| getPkgPipelineInfo | Get info for 'shmootl' pipelines. |
| getPkgPipelineNames | Get 'shmootl' pipeline names. |
| getPkgPipelineUsage | Get default usage string for 'shmootl' pipelines. |
| getPosColDataMapUnit | Get map unit from position column values. |
| getPosColIndex | Get 'mapframe' position column index. |
| getPosColNameMapUnit | Get map unit from position column heading. |
| getQTLFeatures | Get annotation of features within QTL intervals. |
| getQTLIntervals | Get QTL intervals. |
| getQTLPeaks | Get QTL peaks. |
| getResultAnalysesHDF5 | Get names of result analyses for a given phenotype. |
| getResultInfoHDF5 | Get result info for the given HDF5 scan files. |
| getResultNamesHDF5 | Get names of results for a given phenotype and analysis. |
| getResultPhenotypesHDF5 | Get names of result phenotypes in HDF5 file. |
| getRowIndices | Get row indices of object. |
| getRowMask | Get logical mask of object rows. |
| getRunIndexList | Get index list of successive runs in a vector. |
| getRunIndices | Get indices of successive runs in a run-length encoding. |
| getSampleIndices-methods | Get sample indices. |
| getSampleNames-methods | Get sample names. |
| getSamples-methods | Get sample IDs. |
| getSamplesVCF | Get sample IDs from VCF file. |
| getScanoneThresholdInfo | Get 'scanone' threshold info from object. |
| getSeqColIndex | Get sequence column index. |
| getSeqIndices-methods | Get sequence indices. |
| getSeqinfo | Get 'GenomeInfoDb' 'Seqinfo' object. |
| getSeqMarkers-methods | Get markers by sequence. |
| getSeqNames-methods | Get vector of sequence names. |
| getSeqTable | Get genome sequence info table. |
| getSequences-methods | Get vector of normalised sequence labels. |
| getSpecialAttributeNames | Get special attributes for the given object. |
| getStrainIndices-methods | Get strain indices for the given samples. |
| getTetradIndices-methods | Get tetrad indices for the given samples. |
| getXInfoFromFilenames | Get experiment info from filenames. |
| gmapframe | Create a new genetic 'mapframe'. |
| H5Stack-class | An S4 class to manage a HDF5 object stack. |
| h5writeAttributes | Write attributes to HDF5 object. |
| hasCrossHDF5 | Test if HDF5 file contains an 'R/qtl' 'cross' object. |
| hasEnumGenotypes | Test if object contains enumerated genotypes. |
| hasFounderGenotypes | Test if object contains founder genotypes. |
| hasGenoQualVCF | Test if VCF file contains GQ scores. |
| hasMapCSV | Test if CSV file contains map data. |
| hasMapHDF5 | Test if HDF5 file contains the named map. |
| hasMarkerSeqs-methods | Test if 'CrossInfo' object has a marker-sequence mapping. |
| hasNames | Test if object has names. |
| hasObjectHDF5 | Test if HDF5 file contains the named object. |
| hasPhysicalPositions | Test if QTL intervals contain physical positions. |
| hasResultsOverviewHDF5 | Test if HDF5 file contains a QTL analysis results overview. |
| hasRownames | Test if object has rownames. |
| hasSampleIDs-methods | Test if 'CrossInfo' object has sample IDs. |
| hasStrainIndices-methods | Test if 'CrossInfo' object has strain indices. |
| hasTetradIndices-methods | Test if 'CrossInfo' object has sample tetrad indices. |
| hasTimeSeriesPhenotypes | Test if 'cross' contains time-series phenotypes. |
| inferFormatFromFilename | Infer format from filename. |
| inferLodColNames | Infer 'scanone' result LOD column names. |
| inferMapStep | Infer map step size. |
| inferStepSize | Infer step size from step values. |
| inferStrainIndices | Infer sample strain indices. |
| inferTetradIndices | Infer sample tetrad indices. |
| inferTimeStep | Infer time step of time-series phenotypes. |
| initialize-methods | Init 'H5Stack' object. |
| inMapOrder | Test if object is in map order. |
| inRange | Test if numbers lie within a range. |
| insertColumn | Insert column in an object. |
| interpTimeSeries | Interpolate gaps in a time-series. |
| intersectLoci | Find intersection set of loci. |
| isBOOL | Test for a single logical value. |
| isDefaultMarkerID | Test for default marker IDs. |
| isDefaultQTLName | Test for default QTL names. |
| isEnumAllele | Test if symbol is a valid enumerated allele. |
| isEnumGenotype | Test if symbol is a valid enumerated genotype. |
| isFALSE | Test for a single 'FALSE' value. |
| isFounderAllele | Test if symbol is a valid founder allele. |
| isFounderGenotype | Test if symbol is a valid founder genotype. |
| isGeneticMap | Test if object is a genetic 'map'. |
| isGeneticMapframe | Test if object is a genetic 'mapframe'. |
| isGeneticMapUnit | Test if object is a known genetic map unit. |
| is.mapping | Test if object is a 'mapping'. |
| isMarkerID | Test for marker IDs. |
| isNegativeNumber | Test for negative numbers. |
| isNonNegativeNumber | Test for non-negative numbers. |
| isNormChr | Test for normalised chromosome labels. |
| isNormSeq | Test for normalised sequence labels. |
| isPhysicalMap | Test if object is a physical 'map'. |
| isPhysicalMapframe | Test if object is a physical 'mapframe'. |
| isPhysicalMapUnit | Test if object is a known physical map unit. |
| isPositiveNumber | Test for positive numbers. |
| isPositiveWholeNumber | Test for positive whole numbers. |
| isProbability | Test for valid probabilities. |
| isPseudomarkerID | Test for pseudomarker IDs. |
| isRawAllele | Test if symbol is a valid raw SNP allele. |
| isRawGenotype | Test if symbol is a valid raw SNP genotype. |
| isSingleChar | Test for a single character. |
| isSingleFiniteNumber | Test for a single finite number. |
| isSingleNonNegativeNumber | Test for a single non-negative number. |
| isSingleNonNegativeWholeNumber | Test for a single non-negative whole number. |
| isSinglePositiveNumber | Test for a single positive number. |
| isSinglePositiveWholeNumber | Test for a single positive whole number. |
| isSingleProbability | Test for a single valid probability. |
| isSingleString | Test for a single character string. |
| isSingleWholeNumber | Test for a single whole number. |
| isValidAllele | Test if symbol is a valid allele. |
| isValidGenotype | Test if symbol is a valid genotype. |
| isValidID | Test identifier validity. |
| isValidMapUnit | Test if object is a known map unit. |
| isValidName | Test for syntactically valid names. |
| isWholeNumber | Test for whole numbers. |
| joinH5ObjectNameParts | Join components of HDF5 object name. |
| joinSeqLabels | Join sequence labels. |
| listGenomes | List available genomes. |
| listWorksheets | List available output worksheets. |
| loadChrTable | Load chromosome info. |
| loadMapping | Load a mapping from a line or file. |
| loadSeqTables | Load genome sequence info tables. |
| loadVector | Load a vector from a line or file. |
| makeAlleleSet | Make allele set from the given genotypes. |
| makeCross | Make an 'R/qtl' 'cross' object. |
| makeDefaultElementNames | Make default HDF5 group element names. |
| makeDefaultMapName | Get default map name. |
| makeDefaultMarkerIDs | Make default marker IDs for loci. |
| makeDefaultQTLNames | Make default QTL names for the specified loci. |
| makeEnumGenoMatrix | Make enumerated genotype matrix from genotype data. |
| makeFounderGenoMatrix | Make founder genotype matrix from genotype data. |
| makeGeno | Make an 'R/qtl' 'cross' 'geno' object. |
| makeGenotypeSet | Make genotype set from the given alleles and cross type. |
| makeGroupObjectNames | Make valid HDF5 group object names. |
| makeLODBinLabels | Make LOD bin labels from bin starts. |
| makeMapFromDefaultMarkerIDs | Make map from default marker IDs. |
| makeMapFromDefaultQTLNames | Make map from default QTL names. |
| makeMapFromLocusIDs | Make map from locus IDs. |
| makeMapFromPseudomarkerIDs | Make map from pseudomarker IDs. |
| makeNumbers | Make numbers from numeric names. |
| makePlaceholderMap | Make a placeholder map. |
| makePlaceholderPheno | Make a placeholder 'pheno' object. |
| makePseudomarkerIDs | Make pseudomarker IDs for the specified loci. |
| makeResultsOverview | Make QTL analysis results overview. |
| makeScanoneThresholdObject | Make 'scanone' threshold object. |
| makeScantwoThresholdObject | Make 'scantwo' threshold object. |
| makeWorksheetNames | Make 'shmootl' output worksheet names. |
| mapframe | Create a new 'mapframe'. |
| mapkey | Make new 'mapkey' rescaling function. |
| mapkeyOpt | Set/get 'shmootl' 'mapkey' option. |
| mapping | Create a 'mapping' object. |
| mappingKeys | Get keys of a 'mapping' object. |
| mappingValues | Get values of a 'mapping' object. |
| mapsEqual | Test if two 'R/qtl' 'map' objects are essentially equal. |
| matchLoci | Get object loci matching those specified. |
| matchLocusRowIndices | Find matching locus row indices. |
| matchSeqRowIndices | Find row indices of matching sequences. |
| mergeLODBinLabels | Merge multiple vectors of LOD bin labels. |
| nodePermScanone | Run 'qtl::scanone' on a single permuted 'cross' object. |
| nodePermScanoneF | Run 'funqtl::scanoneF' on a single permutation of a 'cross'... |
| nodePermScantwo | Run 'qtl::scantwo' on a single permuted 'cross' object. |
| nodePermScantwoF | Run 'funqtl::scantwoF' on a single permutation of a 'cross'... |
| nodePhenoScanone | Run 'qtl::scanone' on a single phenotype of a 'cross' object. |
| nodePhenoScantwo | Run 'qtl::scantwo' on a single phenotype of a 'cross' object. |
| normChr | Normalise chromosome labels. |
| normSeq | Normalise sequence labels. |
| openStack-methods | Open stack of HDF5 objects. |
| orderChr | Order chromosome labels. |
| orderMap | Put object in map order. |
| orderSeq | Order sequence labels. |
| otherattributes | Get non-reserved object attributes. |
| Package-Constants | Package constants for 'shmootl'. |
| padBins | Pad 'scanonebins' object to given number of bins. |
| padTimeSeries | Pad gaps in a time-series. |
| parseDefaultMarkerIDs | Parse default marker IDs. |
| parseDefaultQTLNames | Parse default QTL names. |
| parseFilenames | Parse filenames by pattern matching. |
| parseLODBinLabels | Parse bin starts from LOD bin labels. |
| parsePseudomarkerIDs | Parse pseudomarker IDs. |
| parseWorksheetNames | Parse 'shmootl' output worksheet names. |
| peek-methods | Get HDF5 object ID at top of 'H5Stack'. |
| permCross | Permute 'cross' phenotype or genotype data. |
| permIndices | Generate permutation indices for a 'cross' object. |
| plotQTLScanone | Plot 'R/qtl' 'scanone' result. |
| plotQTLScantwo | Plot 'R/qtl' 'scantwo' result. |
| plotReportTitlePagePDF | Plot a QTL analysis report title page. |
| pop-methods | Remove HDF5 object ID at top of 'H5Stack'. |
| prepPipelineArgparser | Prep argument parser for 'shmootl' pipeline. |
| print.summary.scanonebins | Print 'summary.scanonebins' object. |
| procPipelineArgs | Process arguments parsed by 'argparser'. |
| pull.alleles | Pull alleles from the given object. |
| pull.chr | Pull chromosomes/sequences from the given object. |
| pull.crosstype | Pull cross type from the given object. |
| pull.ind | Pull individual sample IDs from the given object. |
| pullLoci | Pull loci from object. |
| pullLocusIDs | Pull individual locus IDs. |
| pullLocusPos | Pull individual locus positions. |
| pullLocusSeq | Pull sequence labels for individual loci. |
| pullMap | Pull map from object. |
| pushLoci | Replace loci of object. |
| pushLocusIDs | Replace individual locus IDs. |
| pushLocusPos | Replace individual locus positions. |
| pushLocusSeq | Replace sequence labels of individual loci. |
| pushMap | Push map into object. |
| push-methods | Push HDF5 object ID onto top of 'H5Stack'. |
| qtlintervals | Create a 'qtlintervals' object. |
| rankChr | Rank chromosome labels. |
| rankSeq | Rank sequence labels. |
| readCovarCSV | Read covariate matrix from a CSV file. |
| readCrossCSV | Read yeast 'cross' from a CSV file. |
| readCrossHDF5 | Read 'R/qtl' 'cross' object from an input HDF5 file. |
| readDatasetHDF5 | Read HDF5 dataset. The named HDF5 dataset is read from the... |
| readFeaturesGFF | Read annotation from GFF file. |
| readGenoCSV | Read yeast genotype data from a CSV file. |
| readGenoVCF | Read genotype data from a VCF file. |
| readMapCSV | Read 'map' from a CSV file. |
| readMapframeCSV | Read 'mapframe' from a CSV file. |
| readMapHDF5 | Read 'map' from an input HDF5 file. |
| readObjectAttributesHDF5 | Read HDF5 object attributes. |
| readPhenoCSV | Read yeast phenotype data from a CSV file. |
| readResultHDF5 | Read QTL analysis result from an input HDF5 file. |
| readResultsOverviewHDF5 | Read QTL analysis results overview from an input HDF5 file. |
| readSnpsVCF | Read raw SNP genotypes from VCF files. |
| recodeCSV | Recode 'R/qtl' data in CSV file. |
| refreshCross | Refresh derived data attributes of 'R/qtl' 'cross'. |
| removeColsNA | Remove columns containing only 'NA' values. |
| removeRowsNA | Remove rows containing only 'NA' values. |
| requestNodes | Request nodes for parallel execution. |
| requestPkgDataPath | Request path of 'shmootl' package data. |
| resolveAnalysisTitle | Resolve analysis title. |
| resolveH5ObjectName | Resolve absolute HDF5 object name. |
| resolveMapNameHDF5 | Resolve map name in HDF5 file. |
| resolveScantwoLodtypes | Resolve 'scantwo' LOD types. |
| rstripBlankCols | Strip blank columns from right of 'data.frame'. |
| run | Run shmootl pipeline from the command line. |
| run_annoqtl | Annotate QTL intervals. |
| run_digest | Create digest of QTL analysis results. |
| run_estimap | Estimate map from cross/genotype data. |
| run_interptimes | Interpolate time-series phenotypes in 'R/qtl' CSV file. |
| run_makecross | Make cross CSV file from genotype and phenotype data. |
| run_makegeno | Make genotype data from VCF. |
| run_prep | Prepare data in 'R/qtl' CSV file. |
| run_pullmap | Pull map from a data file. |
| run_pushmap | Push map into a data file. |
| run_recode | Recode data in 'R/qtl' CSV file. |
| run_report | Create report of QTL analysis results. |
| run_scanone | Do single-QTL scan. |
| run_scantwo | Do 2-QTL scan. |
| setAlleles-methods | Set allele symbols. |
| setColumnFromRownames | Move object row names to the specified column. |
| setCrosstype-methods | Set cross type. |
| setGenotypes-methods | Set genotype symbols. |
| setMapUnit | Set map unit. |
| setMarkerSeqs-methods | Set marker sequences. |
| setMarkers-methods | Set markers. |
| setPhenotypes-methods | Set phenotypes. |
| setPosColDataMapUnit | Set map unit of position column data. |
| setPosColNameMapUnit | Set map unit of position column heading. |
| setRownamesFromColumn | Move specified column to object row names. |
| setSamples-methods | Set samples by index or sample ID. |
| setSequences-methods | Set sequences. |
| setStrainIndices-methods | Set strain indices. |
| setTetradIndices-methods | Set sample tetrad indices. |
| setupDefaultMapkeys | Setup default 'mapkey' objects. |
| setValidity-methods | Validate 'CrossInfo' object. |
| shmootl-package | QTL Analysis Utilities for Yeast |
| show-methods | Get number of HDF5 objects in 'H5Stack'. |
| sniffCSV | Identify type of 'R/qtl' data in CSV file. |
| sortChr | Sort chromosome labels. |
| sortSeq | Sort sequence labels. |
| splitH5ObjectName | Split HDF5 object name into component parts. |
| splitSeqLabels | Split sequence labels. |
| stopif | Stop if the expression is 'TRUE'. |
| stripWhite | Strip leading/trailing whitespace from elements of a... |
| subsetByLoci | Subset object by the specified loci. |
| subsetByLocusID | Subset object by locus ID. |
| subsetBySeq | Subset object by the specified sequences. |
| subsetMap | Subset 'shmootl' 'map' object. |
| subset.summary.scanonebins | Subset a 'summary.scanonebins' object. |
| subset.summary.scanoneperm | Subset a 'summary.scanoneperm' object. |
| subset.summary.scantwoperm | Subset a 'summary.scantwoperm' object. |
| summary-methods | Display summary of 'H5Stack' object. |
| summary.scanonebins | Estimate FDR LOD thresholds from a 'scanonebins' object. |
| testQTLPeakSignificance | Test if QTL peaks are significant. |
| updateResultsOverview | Update QTL analysis results overview. |
| validateAlleleSet | Validate a set of alleles. |
| validateAlleles-methods | Validate allele information. |
| validateCrosstype-methods | Validate cross type information. |
| validateGeneticMapUnit | Validate genetic map unit. |
| validateGenotypeSet | Validate a set of genotypes. |
| validateGenotypes-methods | Validate genotype information. |
| validateMap | Validate 'map' object. |
| validateMapframe | Validate 'mapframe' object. |
| validateMapping | Validate a 'mapping' object. |
| validateMapUnit | Validate map unit. |
| validateMarkers-methods | Validate marker information. |
| validatePhenotypes-methods | Validate phenotype information. |
| validatePhysicalMapUnit | Validate physical map unit. |
| validateRawGenoArray | Validate 'array' as containing raw genotype data. |
| validateResultsOverview | Validate a QTL analysis results overview. |
| validateSamples-methods | Validate sample information. |
| validateSequences-methods | Validate sequence information. |
| wasa | WAxSA Cross Data |
| writeCrossCSV | Write yeast 'cross' to a CSV file. |
| writeCrossHDF5 | Write 'R/qtl' 'cross' object to an output HDF5 file. |
| writeDatasetHDF5 | Write R object to an output HDF5 dataset. |
| writeDigestExcel | Write an Excel digest of QTL scan results. |
| writeGenoCSV | Write yeast genotype data to a CSV file. |
| writeMapCSV | Write 'map' to a CSV file. |
| writeMapframeCSV | Write 'mapframe' to a CSV file. |
| writeMapHDF5 | Write 'map' to an output HDF5 file. |
| writeObjectAttributesHDF5 | Write attributes to a HDF5 object. |
| writePhenoCSV | Write yeast pheno data to a CSV file. |
| writeReportExcel | Write an Excel report of QTL scan results. |
| writeReportPDF | Write a PDF report of QTL scan results. |
| writeResultHDF5 | Write QTL analysis result to an output HDF5 file. |
| writeResultsOverviewHDF5 | Write QTL analysis results overview to an output HDF5 file. |
| writeWorkbookExcel | Write an Excel workbook of QTL analysis results. |
