Find breakpoints in Strand-seq data

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Documentation for package ‘breakpointR’ version 1.27.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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