| amp.del | Retrieve amplification events from a 'genecnv.obj' generated... |
| ave.segmean | Obtain the average weighted segment mean log2 ratios from... |
| break.annot-class | Class to store breakpoint annotations in association with... |
| break.density | Generating a genomic map based on a defined bin size and... |
| breaks-class | Class to store breakpoint annotations in association with... |
| chr.arm.cnv | Obtain a matrix with the weighted average CN per chromosome... |
| chromo.regs-class | Class to store shattered regions and information produced by... |
| chromosome.limit.coords | This function mapps defines mapping limmit regions based on a... |
| chr.sort | A function to order a list of chromosomes |
| circ.chromo.plot | Circos plot combining segmentation and SV calls |
| circ.wg.plot | Circos plot combining segmentation and SV calls |
| clean.cnv.artifact | Remove likely artifacts from segmentation data and fill gaps... |
| cnv.break.annot | Identify recurrently altered genes by CNV. The function will... |
| cnv.breaks | Identify CNV breakpoints filtered by the change in copy... |
| cnv.freq | Plot CNV frequency across the genome using a CNV segmentation... |
| cnvfreq-class | Class to store breakpoint annotations in association with... |
| createRandomString | Generates n unique random character strings of a given length |
| d3gb.chr.lim | A function to order a list of chromosomes |
| dngr | generate GRanges of downstream regions |
| freq.p.test | Obtains significance cutoff for the frequency of binary... |
| geneBreakOverlap | Find overlaps between genomic features and SV breakpoints; |
| gene.cnv | Obtain a matrix with the weighted average CN per chromosome... |
| genecnv-class | Class to store breakpoint annotations |
| gene.track.view | Plot genome tracks in local genomic regions |
| get.genesgr | retrieves a GRanges object containinng gene annotations for... |
| hot.spot.samples | Define peak regions and samples in shattered regions hot... |
| IQM | Obtains interquantile average for a defined 'x' vector and... |
| IQSD | Obtains inter quantile standard deviation for a defined 'x'... |
| map2color | Obtains inter quantile average for a defined 'x' vector and... |
| match.breaks | Compare two different sets of breakpoints |
| med.segmean | Obtain the median segment mean from a segmentaton file; The... |
| merge2lists | Given two lists with (or without common names) returns a... |
| null.freq-class | Class to store observed and null distr. as well as ampirical... |
| pct.genome.changed | Calculate the percentage of genome changed by CNV |
| refSeqDat-class | Class to store refseq data from UCSC containing exon level... |
| refseq_hg19 | refSeq annotations for hg19 and hg38 versions from UCSC... |
| segdat_lung_ccle | CCLE degmentation data from breast tissue cell lines |
| segment.gap | Fills the gaps in a segmentation data.frame. Chromosome... |
| shattered.eval | Evaluate shattered regions based on interleaved breaks and... |
| shattered.map.plot | Visualize the aggregate map of shattered regions for all... |
| shattered.regions | Caller for shattered genomic regions based on breakpoint... |
| shattered.regions.cnv | Caller for the identification of shattered genomic regions... |
| svc.break.annot | Identify recurrently altered genes by structural variants.... |
| svc.breaks | Transform structural variant (SVC) data.frame into a 'breaks'... |
| svcnvio-class | Class to store CNV segmentation data |
| sv.model.view | Integrated visualization of SVs and CNVs in local genomic... |
| upgr | generate GRanges of upstream regions |
| validate.cnv | Validate and reformat CNV segmentation input |
| validate.svc | Validate and reformat SV (structural variant) calls input |
