plotAlleleDensity: Plot density/histogram of allele frequencies

In epurdom/cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

Description

Plot of densities/histograms of allele frequencies, useful for evaluating normal contamination estimate, total Copy number estimates, etc.

Usage

plotAlleleDensity(af, depth, groupingId, totalCopy, groupCol=palette(),
	normCont = 0, type="mutation", minDepth = 40, 
	lineCols = c("grey", "tan4"), minMut = 40, 
	histogram = FALSE)

Arguments

af	vector of allele frequencies
depth	coverage of the location
groupingId	grouping variable for allele frequencies (single density curve/histogram for each id)
totalCopy	the total copy number for the allele frequencies plotted (must be the same)
groupCol	colors for the different groups (if histogram=FALSE)
type	type of allele frequency (mutation, SNPHet, SNPHomo), passed to allAF
normCont	percentage of normal contamination. Can be vector of different values.
minDepth	min required depth in order to include it in the density/histogram
lineCols	colors of the vertical lines (each color is for different normal contamination)
minMut	minimum number of mutations per group in order to plot the group
histogram	logical. should the plot be superimposed density curves (FALSE), or a single histogram per group (TRUE)?

Value

Returns invisibly the data used (i.e. passed minimum cutoff criteria), separated by the groupingId given by the user

Author(s)

Elizabeth Purdom

Examples

data(mutData)
#only mutations in the CNLOH region
onlyMuts<-subset(mutData,is.na(rsID) & position <= 1.8E7) 
plotAlleleDensity(onlyMuts$allelefreq,onlyMuts$t_ref_count+onlyMuts$t_alt_count,
	totalCopy=2,normCont=c(0,0.22),minMut=0,minDepth=0,hist=TRUE)

gpId<-factor(is.na(mutData$rsID),levels=c("TRUE","FALSE"),labels=c("Mutations","SNPs"))
plotAlleleDensity(mutData$allelefreq,mutData$t_ref_count+mutData$t_alt_count,
	groupCol=c("black","red"),totalCopy=2,groupingId=gpId,minMut=0,minDepth=30,hist=FALSE)
legend("topleft",levels(gpId),fill=c("red","black"))

epurdom/cancerTiming documentation built on May 16, 2019, 8:21 a.m.