Man pages for nriddiford/svBreaks
Analyse structrual variant breakpoint data as produced by [svParser](https://github.com/nriddiford/svParser)
| bpAllGenes | Calculate the enrichment of genes affected by SVs (as opposed... |
| bpFeatureEnrichment | Calculate the enrichment of SVs in genomic features |
| bpFeatureEnrichmentPlot | Plot the enrichment of SVs in genomic features |
| bpFeatures | bpFeatures Get some basic stats for breakpoints |
| bpGeneEnrichment | Calculate the enrichment of SVs in genes |
| bpGeneEnrichmentPlot | Plot the enrichment of SVs in genes |
| bpRainfall | bpRainfall Plot log10 distances between snvs as rainfall plot |
| bpRegionEnrichment | Calculate the enrichment of SVs in genomic regions |
| bpRegionEnrichmentPlot | Plot the enrichment of SVs in genomic features |
| bpRegioneR | Run regioneR for to regions in bed format |
| bpSim | bpSim |
| bpStats | bpStats Get some basic stats for breakpoints |
| cleanTheme | Set theme for clean plotting with ggplot2 |
| dist2Motif | dist2Motif Calculate the distance from each breakpoint to... |
| dist2motif2 | dist2Motif2 Calculate the distance from each breakpoint to... |
| distOverlay | Calculate the distance from each breakpoint to closest motif... |
| distOverlay2 | Calculate the distance from each breakpoint to closest motif... |
| featureDensity | featureDensity |
| geneHit | Print barplot showing samples with SVs affecting specified... |
| generateData | generateData Prepare data for dist2motif |
| generateData2 | generateData2 Prepare data for dist2motif |
| genesbySample | genesbySample Plot the number of structural breakpoints per... |
| genomeHits | genomeHits |
| genotypeTypeCount | genotypeTypeCount Plot the contribution of sv tpyes to toal... |
| getData | getData |
| getMissingSamples | get sample names |
| ggVolcano | Plot the enrichment of SVs in genomic features |
| hello | Hello, World! |
| mechansimSize | Plot mechanims vs length mechansimSize |
| mergeOverlaps | Implements bedtools merge to merge overlapping regions in... |
| micromologyPlot | Plot micromology vs type micromology |
| notchFilt | Functions related to Notch notchFilt |
| notchHits | notchHits Plot the breakpint density over Notch |
| plot_bpRegioner | Plot overlaps from bpRegioner |
| plotdistanceOverlay | plotdistanceOverlay |
| plotdistanceOverlay2 | plotdistanceOverlay |
| plotMonteCarlo | Plot the result of a monte carlo simulation (n shuffles of... |
| setCols | Set colour scheme for manual colouring |
| showSamples | showSamples |
| simSig | simSig |
| simSig2 | Calculate stats for simulated data |
| sizeDist | sizeDist Plot the size distribution for different types of... |
| slideTheme | Set theme for slide plotting with ggplot2 |
| snv_colours | SNV colours |
| subtractUnmappable | Implements bedtools subtract to remove unmappable regions in... |
| sv_colours | SV colours |
| svsbySample | svsbySample Plot the number of structural breakpoints per... |
| svTypes | svTypes |
| swapSampleNames | Swap sample names |
| tally_hits | Tally type of sv events in specified gene |
| transform_types | Misc functions transform_types |
| Volcano | Plot the enrichment of SVs in genomic features |
| writeBed | Simple function to write out bedfiels - useful for checking... |
