Man pages for breakpointR
Find breakpoints in Strand-seq data
| BreakPoint | BreakPoint object |
| breakpointr | Main function for the 'breakpointR' package |
| breakpointr2UCSC | Export UCSC browser formated files |
| breakpointR-package | Breakpoint detection in Strand-Seq data |
| breakSeekr | Find breakpoints from deltaWs |
| collapseBins | Collapse consecutive bins with the same ID value |
| confidenceInterval | Estimate confidence intervals for breakpoints |
| confidenceInterval.binomial | Estimate confidence intervals for breakpoints |
| createCompositeFile | Create composite Strand-seq file |
| deltaWCalculator | Calculate deltaWs |
| deltaWCalculatorVariousWindows | Calculate deltaWs using various window sizes |
| exportRegions | Function to print WC regions after breakpointR analysis |
| genotype.binom | Assign states to any given region using binomial test. |
| genotype.fisher | Assign states to any given region using Fisher Exact Test. |
| genotyping | Set of functions to genotype regions in between localized... |
| hotspotter | Find hotspots of genomic events |
| insertchr | Insert chromosome for in case it's missing |
| loadFromFiles | Load 'breakpointR' objects from file |
| plotBreakpoints | Plotting genome-wide ideograms 'breakpointR' |
| plotBreakpointsPerChr | Plotting chromosome specific ideograms 'breakpointR' |
| plotHeatmap | Genome wide heatmap of template inheritance states |
| ranges2UCSC | Generates a bedfile from an input GRanges file |
| readBamFileAsGRanges | Import BAM file into GRanges |
| readConfig | Read breakpointR configuration file |
| removeDoubleSCEs | Process double SCE chromosomes: with internal WC region. |
| removeReadPileupSpikes | Remove large spikes in short reads coverage |
| runBreakpointr | Find breakpoints in Strand-seq data |
| summarizeBreaks | Compile breakpoint summary table |
| synchronizeReadDir | Synchronize Strand-seq read directionality |
| transCoord | Transform genomic coordinates |
| writeConfig | Write breakpointR configuration file |
