|
Volcano()
|
Plot the enrichment of SVs in genomic features |
|
bpAllGenes()
|
Calculate the enrichment of genes affected by SVs (as opposed to breakpoint hits) |
|
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 closest motif |
|
dist2motif2()
|
dist2Motif2
Calculate the distance from each breakpoint to closest motif in a directory of files |
|
distOverlay()
|
Calculate the distance from each breakpoint to closest motif
Overlay the same number of random simulated breakpoints |
|
distOverlay2()
|
Calculate the distance from each breakpoint to closest motif
Overlay the same number of random simulated breakpoints |
|
featureDensity()
|
featureDensity |
|
geneHit()
|
Print barplot showing samples with SVs affecting specified gene |
|
generateData()
|
generateData
Prepare data for dist2motif |
|
generateData2()
|
generateData2
Prepare data for dist2motif |
|
genesbySample()
|
genesbySample
Plot the number of structural breakpoints per sample |
|
genomeHits()
|
genomeHits |
|
genotypeTypeCount()
|
genotypeTypeCount
Plot the contribution of sv tpyes to toal load per genotype |
|
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 bedfile |
|
micromologyPlot()
|
Plot micromology vs type
micromology |
|
notchFilt()
|
Functions related to Notch
notchFilt |
|
notchHits()
|
notchHits
Plot the breakpint density over Notch |
|
plotMonteCarlo()
|
Plot the result of a monte carlo simulation (n shuffles of feature y)
Expects dataframe returned from bpRegionEnrichment() |
|
plotdistanceOverlay()
|
plotdistanceOverlay |
|
plotdistanceOverlay2()
|
plotdistanceOverlay |
|
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 structual variants |
|
slideTheme()
|
Set theme for slide plotting with ggplot2 |
|
snv_colours()
|
SNV colours |
|
subtractUnmappable()
|
Implements bedtools subtract to remove unmappable regions in bedfiles |
|
svTypes()
|
svTypes |
|
sv_colours()
|
SV colours |
|
svsbySample()
|
svsbySample
Plot the number of structural breakpoints per sample |
|
swapSampleNames()
|
Swap sample names |
|
tally_hits()
|
Tally type of sv events in specified gene |
|
transform_types()
|
Misc functions
transform_types |
|
writeBed()
|
Simple function to write out bedfiels - useful for checking after merging/subtracting... |