Find breakpoints in Strand-seq data


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Documentation for package ‘breakpointR’ version 1.14.0

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breakpointR-package Breakpoint detection in Strand-Seq data
BreakPoint BreakPoint object
breakpointR Breakpoint detection in Strand-Seq data
breakpointr Main function for the 'breakpointR' package
breakpointr2UCSC Export UCSC browser formated files
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.
GenotypeBreaks Set of functions to genotype regions in between localized breakpoints
genotyping Set of functions to genotype regions in between localized breakpoints
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