Man pages for daewoooo/StrandPhaseR
Phase template strands from Strand-seq data

assembleHapsThis will take sorted matrices and will calculate concordance...
bamregion2GRangesImport BAM file into GRanges
calcMatrixScoreThis function calculates score of a matrix as a sum of...
compareSingleCellHapsThis will take sorted matrices and will calculate concordance...
exportBedGraphGenerates a bedgraph from GRanges object in order to upload...
exportConsensusThis funcion will load sorted watson and crick matrices and...
exportVCFGenerates a VCF file from phased haplotypes
fillGapsThis function will take both assembled haplotypes and will...
loadGRangesFromFilesLoad phased data from RData files
loadMatricesThis funcion will read in partial single cell haplotypes into...
LOHseekerThis function uses circular-binary-segementation to segment...
phaseChromosomeWrapper function for StrandPhaseR
plotHapDensityThis function will take phased data for each chromosome and...
plotPhasedReadsThis function will take phased reads for each chromosome and...
plotSingleCellHapsThis function will take phased data for each chromosome and...
readConfigRead StrandPhaseR configuration file
sortMatricesThis funcion will load initial watson and crick matrices and...
splitReadsThis will take phased info for each haplotype and will split...
strandPhaseRWrapper function
vcf2rangesRead VCF file into a 'GRanges' object
writeConfigWrite StrandPhaseR configuration file
daewoooo/StrandPhaseR documentation built on Dec. 4, 2017, 2:25 p.m.