Man pages for ccbiolab/svpluscnv
svpluscnv: analysis and visualization of complex structural variation data
| amp.del | Amplifications and deletions |
| ave.segmean | Average sample CNV |
| bed2chromo.reg | Transforms a bed format data.frame containing genomic regions... |
| break.annot-class | break.annot class |
| break.density | Breakpoint density map |
| break.iqm-class | Data class break.iqm |
| breaks-class | Data class breaks |
| brk.burden.iqm | Evaluates the breakpoint burden based on a instance 'breaks'... |
| chr.arm.cnv | Chromosome arm mean CNV |
| chromo.regs-class | Data class chromo.regs |
| chromosome.limit.coords | Chromosome limit map |
| chr.sort | Chromosome ordering |
| circ.chromo.plot | Circular visualization of shattered regions |
| circ.wg.plot | Circular visualization CNV and SVC |
| clean.cnv.artifact | CNV artifact detection and filtering |
| cnv_blacklist_regions | Low coverage regions |
| cnv.break.annot | Identification of recurrently altered genes using CNV data... |
| cnv.breaks | Identify CNV breakpoints |
| cnv.freq | CNV frequency map |
| cnvfreq-class | Data class cnvfreq |
| createRandomString | Unique random string generator |
| d3gb.chr.lim | Chromosome start and end |
| dngr | Generate GRanges of downstream regions |
| extract.bins-methods | Return the genomicRanges object containing the genomic bins |
| freq.p.test | Frequency hot spot detection Obtains significance cutoff for... |
| freq.threshold-methods | Return frequency threshold from null.freq object |
| geneBreakOverlap | Find overlaps between genomic features and breakpoints |
| gene.cnv | Gene-level CNV |
| genecnv-class | Data class cnvmat |
| gene.symbol.info-methods | Return coordinates of an specified gene |
| gene.track.view | Gene track visualization |
| get.chr.bins | Generates a GenomicRanges objact containing genomic bins... |
| get.genesgr | Genes GRanges |
| hbd.mat-methods | Return the binary matrix containing high confidence... |
| hot.spot.samples | Hot-spot sample retrieval |
| IQM | Inter-quantile mean |
| IQSD | Inter-quantile standard deviation |
| map2color | Color map from numeric vector |
| match.breaks | Breakpoint matching |
| med.segmean | Median sample CNV |
| merge2lists | Merge two lists |
| nbl_segdat | TARGET Neuroblastoma CNV |
| nbl_svdat | TARGET Neuroblastoma SVC |
| null.freq-class | Data class null.freq |
| pct.genome.changed | Percent genome change calculation |
| refSeqDat-class | Data class refSeqDat |
| refseq_hg19 | Reference transcript and exon annotations for hg19 |
| refseq_hg38 | Reference transcript and exon annotations for hg38 |
| segdat_lung_ccle | Lung CCLE CNV data |
| segment.gap | CNV segmentation gap filling |
| shattered.eval | Evaluate true catastrophic events Evaluate shattered regions... |
| shattered.map.plot | Shattered regions genomic map |
| shattered.regions | Shattered region detection |
| shattered.regions.cnv | CNV-only based shattered region detection |
| svc.break.annot | Identification of recurrently altered genes using SVC data |
| svc.breaks | Identify SVC breakpoints |
| svcnvio-class | Data class svcnvio |
| svdat_lung_ccle | Lung CCLE SVC data |
| sv.model.view | SV integrated visualization |
| upgr | Generate GRanges of upstream regions |
| validate.cnv | Initialization of CNV data |
| validate.svc | Initialization of SVC data |
