plotAlleleByPosition: Plot allele frequencies by position

In cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

Description

Plot observed allele frequencies from sequencing data against their location on the chromosome.

Usage

plotAlleleByPosition(mutData, segmentData = NULL, 
	whChr = 1:22, chromosomeId = "chr", 
	sampleName = NULL, sample = FALSE, tumorAFId, positionId, type = "mutation", 
	startId = "start", endId = "end", segFactorId, tCNId, MarkId, segColors, 
	normCont = NULL,  addData = NULL, addColor="red",col="black",pch=1,lwd=2,
	xlim,ylab="Allele Frequency",...)

Arguments

mutData	data.frame with mutation data set to be plotted
segmentData	(optional) segmentation data
whChr	which chromosome to plot
chromosomeId	column name for chromosome (must be same in all data.frames)
sampleName	id printed on the plot to identify the sample
sample	logical. If true, take only a random sample of 10,000 locations for the chromosome. Can speed up for plotting SNPs.
tumorAFId	column name for the allele frequency in mutData
positionId	column name for the allele location in mutData
type	type of allele frequency plotted (passed to ‘allAF’ in order to create the lines for the expected AF)
startId	column name for the start of the segmentation (in segData)
endId	column name for the end of the segmentation (in segData)
segFactorId	column name for the factor for segmentations (in segData).
tCNId	column name that gives the total copy number for the segmentation (in segData); needed if give normCont to calculated expected AF
MarkId	column name of a column with logical values that identifies segments that should be marked up with hash marks.
segColors	vector of colors for the segmentations. Should be as long as the number of levels of segFactorId
normCont	percent normal contamination. If missing, then lines for the expected AF will not be calculated.
addData	data.frame with another set (example germline SNPs) to be plotted in red
addColor	color for the additional data
lwd	line width of the lines for the expected AF
ylab	label for y-axis
xlim	xlim boundaries. If missing, will be calculated.
col	col for the mutData points
pch	pch for the mutData points
...	arguments passed to initial plotting command.

Value

returns invisibly the vector of colors for the segmentations, useful for making legends (see the example)

Author(s)

Elizabeth Purdom

Examples

data(mutData)
 #only mutations in the CNLOH region
onlyMuts<-subset(mutData,is.na(rsID) & position <= 1.8E7)
	snps<-subset(mutData,!is.na(rsID) )
segData<-data.frame(chromosome="17",start=c(0,1.8e7+1),
	end=c(1.8e7,max(mutData$position)),
	totalCpy=c(2,NA),markRegion=c(FALSE,TRUE))
out<-plotAlleleByPosition(onlyMuts,whChr=17, segmentData=segData,
	tCNId="totalCpy",normCont=0.22, addData=snps,pch=19,
	addColor="grey",MarkId="markRegion",
	segColors="pink",xaxt="n",xlab="Position", segFactorId="totalCpy",
	chromosomeId = "chromosome",tumorAFId="allelefreq", 
	positionId="position",type="mutation") 
axis(1,line=1,tick=FALSE)
legend("topright",legend=c(names(out),"unknown"),fill=c(out,NA),
	title="Total Copy Number")

cancerTiming documentation built on May 2, 2019, 9:28 a.m.