Man pages for daewoooo/StrandPhaseR
Phase template strands from Strand-seq data
| assembleHaps | This will take sorted matrices and will calculate concordance... |
| bamregion2GRanges | Import BAM file into GRanges |
| calcMatrixScore | This function calculates score of a matrix as a sum of... |
| compareSingleCellHaps | This will take sorted matrices and will calculate concordance... |
| 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... |
| exportConsensus | This funcion will load sorted watson and crick matrices and... |
| 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... |
| fillGapsWithVCF | This function will take both assembled haplotypes and will... |
| findRecomb | Find meiotic recombination breakpoints using circular binary... |
| 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... |
| LOHseeker | This function uses circular-binary-segementation to segment... |
| mapRecomb | Map meiotic recombination events in a single family trio... |
| phaseChromosome | Wrapper function for StrandPhaseR to phase a single... |
| phaseHETinversion | Phase a heterozygous inversion using Strand-seq data |
| pipe | Pipe operator |
| plotHapDensity | This function will take phased data for each chromosome and... |
| plotHaploSegs | Plot inherited haplotype segments as ideogram. |
| plotPhasedReads | This function will take phased reads for each chromosome and... |
| plotSingleCellHaps | This function will take phased data for each chromosome and... |
| 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... |
| splitReads | This will take phased info for each haplotype and will split... |
| strandPhaseR | Wrapper function |
| vcf2ranges | Read VCF file into a 'GRanges' object |
| vcf2vranges | Load a VCF file |
| writeConfig | Write StrandPhaseR configuration file |
