makeEventHistory {cancerTiming}R Documentation

Create the event history matrix

Description

Create the event history matrix needed for the event timing algorithm

Usage

makeEventHistory(type = c("gain", "LOH"), copies = NULL, 
	totalCopy = sum(copies), onlyIdentifiable = TRUE)

Arguments

type
copies

a vector of length 2, giving the number of copies of the maternal and paternal chromosomes

totalCopy

an integer between 2 and 5. totalCopy must be the sum of the numbers given for the argument copies

onlyIdentifiable

logical. Only return event matrices corresponding to event histories with identifiable pi[0]?

Value

The A matrix relates allele frequencies to the event history. The vector A pi gives the probabilities of each allele frequency possible for the specified event.

Author(s)

Elizabeth Purdom

References

Purdom, E, et al. (submitted). “Timing Chromosomal Abnormalities within Cancer Samples.”

Examples

makeEventHistory(type="gain",totalCopy=8)
makeEventHistory(type="gain",copies=c(1,4),totalCopy=5,onlyIdentifiable=FALSE)

[Package cancerTiming version 3.1.8 Index]