Analysis of Short Tandem Repeat (STR) Massively Parallel
Sequencing (MPS) Data
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Documentation for package ‘STRMPS’ version 0.5.8
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| 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 |