Man pages for daewoooo/primatR
What the Package Does (TODO)

bam2GRangesImport BAM file into GRanges
bam2statGet basic BAM file statistics
basesPerGenotypePerChrPlot distribution of total sizes of all inversions per...
collapseBinsCollapses consecutive set of ranges with the same value
collapseOverlapsReduce set of overlapping genomic ranges
countProbCalculate probability of a genomic region having WW, CC or WC...
countUniqueReadIDsCount number of unique read IDs in a set of reads.
coveragePerRegionThis function calculates coverage per set of sequencing...
cutISSreadsSplit Iso-seq alignments by aligned exons
eventsPerChrSizeScatterPlots scatter of event counts to chromosome size
exportBedGraphExport aligned reads into a bedgraph
exportINVcallsFunction to export raw inversion calls.
fragments2UCSCExport UCSC browser formated files
genomewideRangesIdeoPlot genome-wide distribution of ranged data. Ranges are...
genotypeRegionsCalculate genotype in a set of genomic ranges
getDisjointOverlapsFunction to group overlapping ranges based on percentage of...
getDisjointOverlapsWeightedFunction to group overlapping ranges based on percentage of...
getGenotypeCalculate genotype for a specific genomic region
getMinDistFunction to calculate minimal distances to user defined...
getReciprocalOverlapsFunction to calculate percentage of reciprocal overlap...
getRegionBoundariesExpand Genomic Ranges into a set of region boundaries
getSegDupOverlapsFunction to calculate percentage overlap between query and...
getTransChromFusionsDetect trans-chromosomal mappings of Iso-seq reads
gr2grPercOverlapFunction to calculate percentage overlap between two ranges...
hotspotterFind hotspots of genomic events
importCallsLoad structural variant calls
importReadsFromCompositeLoad reads from a composite file
insertchrInsert chromosome for in case it's missing
makeBinsSplit genome into bins
permDistanceToFeatureFunction to test significance of ...
plotAlignmentsPerRegionPlot BAM alignments around user defined genomic regions.
plotColumnCountsPlot categorized metacolumns of ranged data.
plotColumnCountsPerChrPlot categorized metacolumns of ranged data per chromosome.
plotCompositeIdeoPlot genome-wide distribution of plus and minus reads.
plotDistanceTreePrepare NJ tree based on data matrix
plotHICregionalPlot HIC contact matrix.
plotLinksPlot significant connections between read pairs
plotNucmerCoordsPlot 'dotplot' of two sequences.
plotOverlapWithRangesPlot number of overlaps between query and subject ranges.
plotReadPairCoveragePlot read-pair coverage profile per breakpoint
plotVennPartitionsPlot size distribution of ranges in all Venn partitions.
plotVennPartitionsGenPlot genotype distribution of ranges in all Venn partitions.
processReadLinksFilter and plot significant connections between read pairs
randomizeRangesFunction to randomize user defined ranges along each...
range2rangeDistanceFunction to calculate distances to user defined ranges
ranges2UCSCGenerates a bedfile from an input GRanges file.
rangesSizeDistributionPlot sorted size distribution of ranged data.
readPairsAsLinksGet significant connections between read pairs
recalcPercOverlapFunction to calculate reciprocal overlap for a set of genomic...
reformatBind consecutive pairs values in vector into a matrix with...
resizeRangesResize genomic ranges to user defined multiple of their...
subtractRegionsFunction to subtract ranges that flank regions of interest
synchronizeReadDirRegionSynchronize Strand-seq read directionality
transCoordTransform genomic coordinates
daewoooo/primatR documentation built on June 27, 2019, 8:55 p.m.