Man pages for gschofl/DR2S
Dual redundant reference sequencing

bampathAccess the path to a bam alignment file.
cacheSave a DR2S object.
checkAlignmentFileManually check the alignment of consensus sequences using an...
checkHomopolymerCountGet a distribution of homopolymer counts in alleles
clearClear the output directory of a DR2S object.
conseqConstruct a consensus sequence
consmatConstruct a consensus matrix from pileup.
consnameAccess the consensus name.
conspathAccess the path to a consensus sequence file.
createDR2SConfCreate a 'DR2S' configuration object.
createIgvConfigsCreate IGV xml config files for directly open the longread...
createIgvJsFilesCreate subsampled bam files and fasta index files for igv.js...
createPWMCreate position weight matrix from multiple sequence...
disambiguateVariantDisambiguate a variant
dot-generateReferenceSequenceGenerate reference sequences in a FASTA file
dot-getIdleCoresGet the number of idling cores that can be used by calling...
DR2SDR2S - Dual redundant reference sequencing.
DR2S_Class '"DR2S"'
getSRPartitionScoresGet a score for each shortread in a bam file on specific...
hammingDistConstruct a hamming distance matrix from an aligned...
HapPartHapPart (Haplotype Partition) stores the haplotype...
InitDR2SInitialise a 'DR2S' mapper.
mapFinalFinal mapping (long reads and short reads).
mapInitInitial mapping.
mapIterIterative mapping.
MergeEnvConstructor for 'MergeEnv' objects.
MergeEnv_Class '"MergeEnv"'
metaAccess the metadata of an object.
partitionLongreadsPartition mapped long reads into haplotypes
partitionReadsCluster a SNP matrix into haplotype groups
partitionShortreadsAssign short reads from mapInit to haplotypes
pileupCalculate pileup for a BAM file.
plotDiagnosticAlignmentPlot an alignment of all intermediate sequences and reference
plotPartitionHistogramPlot distribution of haplotype partitioned reads
plotPartitionHistogramMultiPlot distribution of haplotype partitioned reads for more...
plotPartitionTreePlot tree of initial clustering
plotPileupBasecallFrequencyPlot basecall frequency
plotPileupCoveragePlot pileup coverage
plotRadarPartitionPlot a radar chart for each haplotype. Membership values for...
polishPolish final haplotype sequences.
polymorphicPositionsCalculate polymorphic positions from a consensus matrix.
readDR2SRead a cached DR2S object
readDR2SConfRead a DR2S config file in yaml or json format
readMSARead a multiple sequence alignment from file.
readpathAccess the path to a read sequence file.
readtypeAccess the readtype.
reexportsObjects exported from other packages
refineAlignmentRefine the mapping of an allele by remapping to the checked...
refnameAccess the reference name.
refpathAccess the path to a reference sequence file.
reportReport the final haplotype sequences.
reportCheckedConsensusReport haplotype consensus files as verified
scoreHighestSRGet the highest scoring haplotype for each read
SNPmatrixConstruct a SNP matrix.
statsAccess the stats of an object.
subSampleBamSubsample a bam file according to coverage
tagAccess the name tag of an object.
writeDR2SConfWrite the DR2S config as yaml or jsoon.
writeMSAWrite a multiple sequence alignment in a phylip like format....
gschofl/DR2S documentation built on Dec. 19, 2018, 8:04 a.m.