| MatrixModel {TE} | R Documentation |
Implements the matrix model in Promislow et al (1999)
Description
Implements the matrix model in Promislow et al (1999)
Usage
MatrixModel(mismatch, len, nsolo, r = 0.013, plotFit = FALSE,
main = sprintf("n = %d", n))
Arguments
mismatch |
A vector containing the number of mismatches. |
len |
A vector containing the length of each element. |
nsolo |
An integer giving the number of solo elements. |
r |
Mutation rate (substitutions/(million year * site)) used in the calculation. |
plotFit |
Whether to plot the distribution fits. |
main |
The title for the plot. |
Details
For the method implemented see References.
Value
This function returns various parameter estimates described in Promislow et al. (1999), containing the following fields. The unit for time is million years ago (Mya):
B |
The constant insertion rate |
q |
The constant excision rate |
lam |
The population growth rate |
R |
The ratio of the number of elements in class j over class j+1, which is constant by assumption |
age1 |
The age of the system under model 1 (lambda > 1) |
age2 |
The age of the system under model 2 (an initial burst followed by stasis lambda = 1) |
References
Promislow, D., Jordan, K. and McDonald, J. "Genomic demography: a life-history analysis of transposable element evolution." Proceedings of the Royal Society of London B: Biological Sciences 266, no. 1428 (1999): 1555-1560.
Examples
# Analyze Gypsy family 24 (Nusif)
data(AetLTR)
dat <- subset(AetLTR, GroupID == 24 & !is.na(Chr))
res1 <- MatrixModel(dat$Mismatch, dat$UngapedLen, nsolo=450, plotFit=TRUE)