Phase template strands from Strand-seq data

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Documentation for package ‘StrandPhaseR’ version 0.99

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assembleHaps This will take sorted matrices and will calculate concordance of each single cell to the consensus haplotypes in order to assemble highly accurate haplotypes
bamregion2GRanges Import BAM file into GRanges
calcMatrixScore This function calculates score of a matrix as a sum of partial scores of each columns
compareSingleCellHaps This will take sorted matrices and will calculate concordance of each single cell to the consensus haplotypes in order to assemble highly accurate haplotypes
correctHetInv Correct heterozygous inversion in StrandPhaseR VCF file.
correctHomInv Correct homozygous inversion in StrandPhaseR VCF file.
correctInvertedRegionPhasing Correct StrandPhaseR phasing over inverted regions
exportBedGraph Generates a bedgraph from GRanges object in order to upload on to UCSC Genome browser
exportConsensus This funcion will load sorted watson and crick matrices and will collapsed them in order to obtain consensus string of each matrix
exportPhasedReads Export Strand-seq phased reads in FASTA or FASTQ format.
exportVCF Generates a VCF file from phased haplotypes
fillGapsWithBam This function will take both assembled haplotypes and will try to fill gaps at positions where only one allele is phased Such position have to be heterozygous so the alternative allele at this position can be reliably distinguished
fillGapsWithVCF This function will take both assembled haplotypes and will try to fill gaps at positions where only one allele is phased Such position have to be heterozygous so the alternative allele at this position can be reliably distinguished
findRecomb Find meiotic recombination breakpoints using circular binary segmentation (CBS)
genotypeStrandScells Genotype Strand-seq cell based on population genotypes.
loadGRangesFromFiles Load phased data from RData files
loadMatrices This funcion will read in partial single cell haplotypes into two parallel matrices separately for Watson and Crick reads
LOHseeker This function uses circular-binary-segementation to segment single cell haplotypes based on their similarity to consensus haploypes of all cells.
mapRecomb Map meiotic recombination events in a single family trio [father-mother-child].
phaseChromosome Wrapper function for StrandPhaseR to phase a single chromosome.
phaseHETinversion Phase a heterozygous inversion using Strand-seq data
plotHapDensity This function will take phased data for each chromosome and plot density of phased SNVs
plotHaploSegs Plot inherited haplotype segments as ideogram.
plotPhasedReads This function will take phased reads for each chromosome and plot them
plotSingleCellHaps This function will take phased data for each chromosome and plot density of phased SNVs
readConfig Read StrandPhaseR configuration file
sliceRanges Slice a certain length from a set of genomic ranges.
sortMatrices This funcion will load initial watson and crick matrices and will sort them according to the phase information of each single cell
splitReads This will take phased info for each haplotype and will split directional reads of each single cell into haplotype specific reads
strandPhaseR Wrapper function
vcf2ranges Read VCF file into a 'GRanges' object
vcf2vranges Load a VCF file
writeConfig Write StrandPhaseR configuration file