BLMM |
Block length of the missing motif. |
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-method |
Find neighbours |
findStutter |
Find stutters |
findStutter-method |
Find stutters |
flankingRegions |
Flanking regions |
genotypeIdentifiedList-class |
Genotype list |
genotypeList |
Genotype list |
getGenotype |
Assigns genotype. |
getGenotype-method |
Assigns genotype. |
identifiedSTRs |
Identified STR regions |
identifyNoise |
Idenfities the noise. |
identifyNoise-method |
Idenfities the noise. |
identifySTRRegions |
Identify the STR regions of a fastq-file or ShortReadQ-object. |
identifySTRRegions-method |
Identify the STR regions of a fastq-file or ShortReadQ-object. |
identifySTRRegions-method |
Identify the STR regions of a fastq-file or ShortReadQ-object. |
identifySTRRegions.control |
Control function for identifySTRRegions |
mergeGenotypeStringCoverage |
Merge genotypeIdentifiedList and stringCoverageList. |
mergeGenotypeStringCoverage-method |
Merge genotypeIdentifiedList and stringCoverageList. |
mergeNoiseStringCoverage |
Merge noiseIdentifiedList and stringCoverageList. |
mergeNoiseStringCoverage-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 |
solexaQualityProbability |
Quality score to probability |
solexaQualityScore |
Convert probability to quality score |
stringCoverage |
Get string coverage STR identified objects. |
stringCoverage-method |
Get string coverage STR identified objects. |
stringCoverage-method |
Get string coverage STR identified objects. |
stringCoverage-method |
Get string coverage STR identified objects. |
stringCoverage-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 |
STRMPSWorkflow |
Workflow function |
STRMPSWorkflowBatch |
Batch wrapper for the workflow function |
STRMPSWorkflowCollectStutters |
Collect stutters files |
workflow.control |
Workflow default options |