Man pages for gschofl/DR2S
Dual redundant reference sequencing
| bampath | Access the path to a bam alignment file. |
| cache | Save a DR2S object. |
| checkAlignmentFile | Manually check the alignment of consensus sequences using an... |
| checkHomopolymerCount | Get a distribution of homopolymer counts in alleles |
| clear | Clear the output directory of a DR2S object. |
| conseq | Construct a consensus sequence |
| consmat | Construct a consensus matrix from pileup. |
| consname | Access the consensus name. |
| conspath | Access the path to a consensus sequence file. |
| createDR2SConf | Create a 'DR2S' configuration object. |
| createIgvConfigs | Create IGV xml config files for directly open the longread... |
| createIgvJsFiles | Create subsampled bam files and fasta index files for igv.js... |
| createPWM | Create position weight matrix from multiple sequence... |
| disambiguateVariant | Disambiguate a variant |
| dot-generateReferenceSequence | Generate reference sequences in a FASTA file |
| dot-getIdleCores | Get the number of idling cores that can be used by calling... |
| DR2S | DR2S - Dual redundant reference sequencing. |
| DR2S_ | Class '"DR2S"' |
| getSRPartitionScores | Get a score for each shortread in a bam file on specific... |
| hammingDist | Construct a hamming distance matrix from an aligned... |
| HapPart | HapPart (Haplotype Partition) stores the haplotype... |
| InitDR2S | Initialise a 'DR2S' mapper. |
| mapFinal | Final mapping (long reads and short reads). |
| mapInit | Initial mapping. |
| mapIter | Iterative mapping. |
| MergeEnv | Constructor for 'MergeEnv' objects. |
| MergeEnv_ | Class '"MergeEnv"' |
| meta | Access the metadata of an object. |
| partitionLongreads | Partition mapped long reads into haplotypes |
| partitionReads | Cluster a SNP matrix into haplotype groups |
| partitionShortreads | Assign short reads from mapInit to haplotypes |
| pileup | Calculate pileup for a BAM file. |
| plotDiagnosticAlignment | Plot an alignment of all intermediate sequences and reference |
| plotPartitionHistogram | Plot distribution of haplotype partitioned reads |
| plotPartitionHistogramMulti | Plot distribution of haplotype partitioned reads for more... |
| plotPartitionTree | Plot tree of initial clustering |
| plotPileupBasecallFrequency | Plot basecall frequency |
| plotPileupCoverage | Plot pileup coverage |
| plotRadarPartition | Plot a radar chart for each haplotype. Membership values for... |
| polish | Polish final haplotype sequences. |
| polymorphicPositions | Calculate polymorphic positions from a consensus matrix. |
| readDR2S | Read a cached DR2S object |
| readDR2SConf | Read a DR2S config file in yaml or json format |
| readMSA | Read a multiple sequence alignment from file. |
| readpath | Access the path to a read sequence file. |
| readtype | Access the readtype. |
| reexports | Objects exported from other packages |
| refineAlignment | Refine the mapping of an allele by remapping to the checked... |
| refname | Access the reference name. |
| refpath | Access the path to a reference sequence file. |
| report | Report the final haplotype sequences. |
| reportCheckedConsensus | Report haplotype consensus files as verified |
| scoreHighestSR | Get the highest scoring haplotype for each read |
| SNPmatrix | Construct a SNP matrix. |
| stats | Access the stats of an object. |
| subSampleBam | Subsample a bam file according to coverage |
| tag | Access the name tag of an object. |
| writeDR2SConf | Write the DR2S config as yaml or jsoon. |
| writeMSA | Write a multiple sequence alignment in a phylip like format.... |
