Man pages for daewoooo/primatR
What the Package Does (TODO)
| bam2GRanges | Import BAM file into GRanges |
| bam2stat | Get basic BAM file statistics |
| basesPerGenotypePerChr | Plot distribution of total sizes of all inversions per... |
| collapseBins | Collapses consecutive set of ranges with the same value |
| collapseOverlaps | Reduce set of overlapping genomic ranges |
| countProb | Calculate probability of a genomic region having WW, CC or WC... |
| countUniqueReadIDs | Count number of unique read IDs in a set of reads. |
| coveragePerRegion | This function calculates coverage per set of sequencing... |
| cutISSreads | Split Iso-seq alignments by aligned exons |
| estimateCN | Estimate copy number (CN) in genomic regions |
| eventsPerChrSizeScatter | Plots scatter of event counts to chromosome size |
| exportBedGraph | Export aligned reads into a bedgraph |
| exportINVcalls | Function to export raw inversion calls. |
| fragments2UCSC | Export UCSC browser formated files |
| genomewideRangesIdeo | Plot genome-wide distribution of ranged data. Ranges are... |
| genotypeRegions | Calculate genotype in a set of genomic ranges |
| getCommonSubrangeSize | Function to calculate a common subrange shared among a set of... |
| getDisjointOverlaps | Function to group overlapping ranges such that common range... |
| getDisjointOverlapsWeighted | Function to group overlapping ranges based on percentage of... |
| getGenotype | Calculate genotype for a specific genomic region |
| getHIContactCounts | Construct HIC contact matrix. |
| getMinDist | Function to calculate minimal distances to user defined... |
| getRangesOverlaps | Function to calculate percentage overlap between query and... |
| getReciprocalOverlaps | Function to calculate percentage of reciprocal overlap... |
| getRegionBoundaries | Expand genomic Ranges into a set of region boundaries |
| getSegDupOverlaps | Function to calculate percentage overlap between query and... |
| getTransChromFusions | Detect trans-chromosomal mappings of Iso-seq reads |
| gr2grPercOverlap | Function to calculate percentage overlap between two ranges... |
| hotspotter | Find hotspots of genomic events |
| importCalls | Load structural variant calls |
| importReadsFromComposite | Load reads from a composite file |
| insertchr | Insert chromosome for in case it's missing |
| makeBins | Split genome into bins |
| permDistanceToFeature | Function to test significance of ... |
| plotAlignmentsPerRegion | Plot BAM alignments around user defined genomic regions. |
| plotColumnCounts | Plot categorized metacolumns of ranged data. |
| plotColumnCountsPerChr | Plot categorized metacolumns of ranged data per chromosome. |
| plotCompositeIdeo | Plot genome-wide distribution of plus and minus reads. |
| plotDistanceTree | Prepare NJ tree based on data matrix |
| plotHICcontactTable | Plot horizontal HIC contact matrix. |
| plotHICregional | Construct and plot HIC contact matrix. |
| plotLinks | Plot significant connections between read pairs |
| plotNucmerCoords | Plot 'dotplot' of two sequences. |
| plotOverlapWithRanges | Plot number of overlaps between query and subject ranges. |
| plotReadPairCoverage | Plot read-pair coverage profile per breakpoint |
| plotSSEQReadsPerRegion | Plot Strand-seq BAM alignments within a user defined set of... |
| plotVennPartitions | Plot size distribution of ranges in all Venn partitions. |
| plotVennPartitionsGen | Plot genotype distribution of ranges in all Venn partitions. |
| processReadLinks | Filter and plot significant connections between read pairs |
| randomizeRanges | Function to randomize user defined ranges along each... |
| range2rangeDistance | Function to calculate distances to user defined ranges |
| ranges2UCSC | Generates a bedfile from an input GRanges file. |
| rangesSizeDistribution | Plot sorted size distribution of ranged data. |
| readPairsAsLinks | Get significant connections between read pairs |
| recalcPercOverlap | Function to calculate reciprocal overlap for a set of genomic... |
| reformat | Bind consecutive pairs values in vector into a matrix with... |
| removeRanges | Function to subtract set of genomic ranges from other genomic... |
| reportOverlapBases | This function will take in a 'GRanges-class' object of... |
| resizeRanges | Resize genomic ranges to user defined multiple of their... |
| subtractRegions | Function to subtract ranges that flank regions of interest |
| synchronizeReadDirRegion | Synchronize Strand-seq read directionality |
| transCoord | Transform genomic coordinates |
