Description Usage Arguments Value Author(s) Examples
Create bootstrap estimates of pi base on the results of a call to eventTiming.
1 2 | bootstrapEventTiming(eventOrdering, B, type = c("parametric",
"nonparametric"), pi, x, m ,call)
|
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) |
Matrix of dimension (B,length(pi)) with the estimate of pi for each of the bootstrap samples
Elizabeth Purdom
1 2 3 4 5 6 7 8 | ##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")
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