cancerTiming (version 3.1.8)

readSimulation: Simulate reads based on an event matrix

Description

Simulate reads based on an event matrix

Usage

readSimulation(B, alleleSet, q, totalCopy, mutRate = NULL, seqError = 0, 
	fixedN = FALSE, normCont = 0, aveReadCoverage = 30, countDistribution = NULL)

Arguments

B

the number of simulated data sets to make

alleleSet

a vector of expected allele frequencies, without contamination or sequencing error accounted for

q

integer. the number of expected allele frequencies???

totalCopy

integer. The total number of copies in the final stage, i.e. at the end of the event

mutRate

a number between 0 and 1. The mutation rate, defined as the number of mutations observed divided by number of nucleotides sequenced or examined

seqError

a number between 0 and 1 representing the sequencing error. The default value is 0, i.e. no sequencing error.

fixedN

logical. Should the number of mutations be fixed? By default set to FALSE. If set to TRUE, the expected number of mutations is used, i.e. mutRate*B

normCont

a number between 0 and 1 describing the amount of normal contamination present in the sample. The default value is 0, i.e. no normal contamination.

aveReadCoverage

average read coverage of an allele. The default value is 30 reads per allele.

countDistribution

optional. Provide an empirical distribution for read coverage. If given, the argument aveReadCoverage is ignored, and the mean of the empirical distribution is used. By default, set to NULL.

Value

• Returns a data frame with simulated read counts under the normal contamination, sequencing error, allele frequency distribution, and read count distributions provided.

Examples

#simulate from CNLOH event with pi[0]=.1
	Amat<-makeEventHistory(totalCopy=2,type="LOH")[[1]]
	piVal<-c(.1,.9)
	qvec<-prop.table(Amat%*%piVal)

	sims<-readSimulation(10, alleleSet=allAF(totalCopy=2)[[1]], q=qvec, 
	totalCopy=2, mutRate = 100, seqError = 0.1, fixedN = TRUE, 
	normCont = 0.1, aveReadCoverage = 30)