Man pages for nriddiford/mutationProfiles
Collection of functions to explore SNV data (e.g. Mutect2/Freebayes) parsed by get_tris.pl

bpRegionEnrichmentPlotPlot the enrichment of SVs in genomic features
bpSimbpSim
chromDistchromDist
cleanThemecleanTheme
dist2motif2dist2Motif2 Calculate the distance from each breakpoint to...
distOverlay2Calculate the distance from each breakpoint to closest motif...
EnrichmentVolcanoPlot the enrichment of SNVs in genes features
featureEnrichmentfeatureEnrichment
featuresHitfeaturesHit
geneEnrichmentgeneEnrichment
geneHitgeneHit
generateDatagenerateData Prepare data for dist2motif
genTrisgenTris
getDatagetData
getTriFromFastaA function to calculate trinucleotide frequences from a...
ggVolcanoPlot the enrichment of SVs in genomic features
indel_lengthsindel_length
mergeOverlapsImplements bedtools merge to merge overlapping regions in...
mutSigsmutSigs
mutSpectrummutSpectrum
plotdistanceOverlay2plotdistanceOverlay
plot_indelsindel_count
plotMonteCarloPlot the result of a monte carlo simulation (n shuffles of...
plot_snvssplot_snvs
rainfallrainfall
samplesPlotsamplesPlot
setColssetCols
showSamplesshowSamples
sigTypessigTypes
snvinGenesnvinGene
snvRegionEnrichmentCalculate the enrichment of SVs in genomic regions
snvSimsnvSim
snvStatssnvStats
subtractUnmappableImplements bedtools subtract to remove unmappable regions in...
triFreqtriFreq
tssDisttssDist
VolcanoPlot the enrichment of SVs in genomic features
writeBedSimple function to write out bedfiels - useful for checking...
nriddiford/mutationProfiles documentation built on Nov. 8, 2019, 6:22 p.m.