cancerTiming (version 3.1.8)

plotAlleleDensity: Plot density/histogram of allele frequencies

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

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"))