Man pages for nriddiford/mutationProfiles
Collection of functions to explore SNV data (e.g. Mutect2/Freebayes) parsed by get_tris.pl
| bpRegionEnrichmentPlot | Plot the enrichment of SVs in genomic features |
| bpSim | bpSim |
| chromDist | chromDist |
| cleanTheme | cleanTheme |
| dist2motif2 | dist2Motif2 Calculate the distance from each breakpoint to... |
| distOverlay2 | Calculate the distance from each breakpoint to closest motif... |
| EnrichmentVolcano | Plot the enrichment of SNVs in genes features |
| featureEnrichment | featureEnrichment |
| featuresHit | featuresHit |
| geneEnrichment | geneEnrichment |
| geneHit | geneHit |
| generateData | generateData Prepare data for dist2motif |
| genTris | genTris |
| getData | getData |
| getTriFromFasta | A function to calculate trinucleotide frequences from a... |
| ggVolcano | Plot the enrichment of SVs in genomic features |
| indel_lengths | indel_length |
| mergeOverlaps | Implements bedtools merge to merge overlapping regions in... |
| mutSigs | mutSigs |
| mutSpectrum | mutSpectrum |
| plotdistanceOverlay2 | plotdistanceOverlay |
| plot_indels | indel_count |
| plotMonteCarlo | Plot the result of a monte carlo simulation (n shuffles of... |
| plot_snvs | splot_snvs |
| rainfall | rainfall |
| samplesPlot | samplesPlot |
| setCols | setCols |
| showSamples | showSamples |
| sigTypes | sigTypes |
| snvinGene | snvinGene |
| snvRegionEnrichment | Calculate the enrichment of SVs in genomic regions |
| snvSim | snvSim |
| snvStats | snvStats |
| subtractUnmappable | Implements bedtools subtract to remove unmappable regions in... |
| triFreq | triFreq |
| tssDist | tssDist |
| Volcano | Plot the enrichment of SVs in genomic features |
| writeBed | Simple function to write out bedfiels - useful for checking... |
