makeEventHistory: Create the event history matrix

In cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

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)

Example output

[[1]]
     [,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,]    1    2    3    4    5    6    8
[2,]    0    0    0    0    0    1    0
[3,]    0    0    0    0    1    0    0
[4,]    0    0    0    1    0    0    0
[5,]    0    0    1    0    0    0    0
[6,]    0    1    0    0    0    0    0
[7,]    1    0    0    0    0    0    0

$`1MLineage x 3`
     [,1] [,2] [,3] [,4]
[1,]    1    2    3    5
[2,]    0    0    1    0
[3,]    0    1    0    0
[4,]    1    0    0    0

$`1MLineage x 2,2MLineage`
     [,1] [,2] [,3] [,4]
[1,]    1    1    3    5
[2,]    0    2    1    0
[3,]    0    0    0    0
[4,]    1    0    0    0

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