Files in daewoooo/primatR

What the Package Does (TODO)

R/bam2GRanges.R R/bam2stat.R R/cutISSreads.R R/estimateCN.R R/export.R R/exportBedGraph.R R/genotypeRegions.R R/getDisjointOverlaps.R R/getReciprocalOverlaps.R R/getSegDupOverlaps.R R/getTransChromFusions.R R/hotspotter.R R/import.R R/permTest.R R/plotting.R R/processHICdata.R R/processReadLinks.R R/randomizeRanges.R R/range2rangeDistance.R R/readPairsAsLinks.R R/removeRanges.R R/reportOverlapBases.R R/subtractRegions.R R/synchronizeReadDirRegion.R R/undocumentedFunctions.R R/utils.R README.md man/bam2GRanges.Rd man/bam2stat.Rd man/basesPerGenotypePerChr.Rd man/collapseBins.Rd man/collapseOverlaps.Rd man/countProb.Rd man/countUniqueReadIDs.Rd man/coveragePerRegion.Rd man/cutISSreads.Rd man/estimateCN.Rd man/eventsPerChrSizeScatter.Rd man/exportBedGraph.Rd man/exportINVcalls.Rd man/fragments2UCSC.Rd man/genomewideRangesIdeo.Rd man/genotypeRegions.Rd man/getCommonSubrangeSize.Rd man/getDisjointOverlaps.Rd man/getDisjointOverlapsWeighted.Rd man/getGenotype.Rd man/getHIContactCounts.Rd man/getMinDist.Rd man/getRangesOverlaps.Rd man/getReciprocalOverlaps.Rd man/getRegionBoundaries.Rd man/getSegDupOverlaps.Rd man/getTransChromFusions.Rd man/gr2grPercOverlap.Rd man/hotspotter.Rd man/importCalls.Rd man/importReadsFromComposite.Rd man/insertchr.Rd man/makeBins.Rd man/permDistanceToFeature.Rd man/plotAlignmentsPerRegion.Rd man/plotColumnCounts.Rd man/plotColumnCountsPerChr.Rd man/plotCompositeIdeo.Rd man/plotDistanceTree.Rd man/plotHICcontactTable.Rd man/plotHICregional.Rd man/plotLinks.Rd man/plotNucmerCoords.Rd man/plotOverlapWithRanges.Rd man/plotReadPairCoverage.Rd man/plotSSEQReadsPerRegion.Rd man/plotVennPartitions.Rd man/plotVennPartitionsGen.Rd man/processReadLinks.Rd man/randomizeRanges.Rd man/range2rangeDistance.Rd man/ranges2UCSC.Rd man/rangesSizeDistribution.Rd man/readPairsAsLinks.Rd man/recalcPercOverlap.Rd man/reformat.Rd man/removeRanges.Rd man/reportOverlapBases.Rd man/resizeRanges.Rd man/subtractRegions.Rd man/synchronizeReadDirRegion.Rd man/transCoord.Rd