BLMM                    Block length of the missing motif.
STRMPSWorkflow          Workflow function
STRMPSWorkflowBatch     Batch wrapper for the workflow function
STRMPSWorkflowCollectStutters
                        Collect stutters files
extractedReadsList-class
                        Extract STR region information
extractedReadsListCombined-class
                        Combined extract STR region information.
extractedReadsListNonCombined-class
                        Combined extract STR region information.
extractedReadsListReverseComplement-class
                        Extract STR region information of the reverse
                        complement DNA strand.
findNeighbours          Find neighbours
findNeighbours,stringCoverageGenotypeList-method
                        Find neighbours
findStutter             Find stutters
findStutter,stringCoverageGenotypeList-method
                        Find stutters
flankingRegions         Flanking regions
genotypeIdentifiedList-class
                        Genotype list
genotypeList            Genotype list
getGenotype             Assigns genotype.
getGenotype,stringCoverageList-method
                        Assigns genotype.
identifiedSTRs          Identified STR regions
identifyNoise           Idenfities the noise.
identifyNoise,stringCoverageList-method
                        Idenfities the noise.
identifySTRRegions      Identify the STR regions of a fastq-file or
                        ShortReadQ-object.
identifySTRRegions,ShortReadQ-method
                        Identify the STR regions of a fastq-file or
                        ShortReadQ-object.
identifySTRRegions,character-method
                        Identify the STR regions of a fastq-file or
                        ShortReadQ-object.
identifySTRRegions.control
                        Control function for identifySTRRegions
mergeGenotypeStringCoverage
                        Merge genotypeIdentifiedList and
                        stringCoverageList.
mergeGenotypeStringCoverage,genotypeIdentifiedList-method
                        Merge genotypeIdentifiedList and
                        stringCoverageList.
mergeNoiseStringCoverage
                        Merge noiseIdentifiedList and
                        stringCoverageList.
mergeNoiseStringCoverage,noiseIdentifiedList-method
                        Merge noiseIdentifiedList and
                        stringCoverageList.
neighbourList-class     A neighbour list
noiseIdentifiedList-class
                        Noise list
noiseList               Noise list
phredQualityProbability
                        Quality score to probability
phredQualityScore       Convert probability to quality score
stringCoverage          Get string coverage STR identified objects.
stringCoverage,extractedReadsList-method
                        Get string coverage STR identified objects.
stringCoverage,extractedReadsListCombined-method
                        Get string coverage STR identified objects.
stringCoverage,extractedReadsListNonCombined-method
                        Get string coverage STR identified objects.
stringCoverage,extractedReadsListReverseComplement-method
                        Get string coverage STR identified objects.
stringCoverage.control
                        String coverage coontrol object
stringCoverageGenotypeList
                        Combined string coverage and genotype
                        information
stringCoverageGenotypeList-class
                        Combined stringCoverage- and
                        genotypeIdentifiedList
stringCoverageList      Aggregated string coverage.
stringCoverageList-class
                        A string coverage list
stringCoverageNoiseList-class
                        Combined stringCoverage- and
                        noiseIdentifiedList
workflow.control        Workflow default options
