bootstrapEventTiming {cancerTiming}

Bootstrap the results of eventTiming

Description

Create bootstrap estimates of pi base on the results of a call to eventTiming.

Usage

 bootstrapEventTiming(eventOrdering, B, type = c("parametric",
                 "nonparametric"), pi, x, m ,call)

Arguments

eventOrdering

output from eventTiming

B

number of bootstrap samples to take

type

type of bootstrap confidence interval to calculate, one of “parametric", “nonparametric"

pi

the estimate of $pi$ from which to create bootstrap samples (if type="parametric". If not given, will use output from eventOrdering)

x

vector. the number of reads/fragments containing the variant; not needed if output from eventOrdering given.

m

vector. the number of reads/fragments covering the location with the variant (the coverage); not needed if output from eventOrdering given.

call

information about the call given to original eventTiming command. Only needed if eventOrdering object not given (mainly used for internal calls within eventTiming function)

Value

Matrix of dimension (B,length(pi)) with the estimate of pi for each of the bootstrap samples

Author(s)

Elizabeth Purdom

Examples

##can do this within eventTiming function, but here is an example doing it separately...
data(mutData)
ACNLOH<-matrix(c(1,3,1,0),ncol=2,nrow=2,byrow=TRUE)
onlyMuts<-subset(mutData,is.na(rsID) & position <= 1.8E7)
onlyMuts$t_depth<-onlyMuts$t_ref_count+onlyMuts$t_alt_count
x<-eventTiming(x=onlyMuts$t_alt_count,m=onlyMuts$t_depth,
    history=ACNLOH,totalCopy=2,type="CNLOH",normCont=0.22,returnAssignments=TRUE)
piBoot<-bootstrapEventTiming(x,B=100,type="parametric")