MatrixModel: Implements the matrix model in Promislow et al (1999)

In TE: Insertion/Deletion Dynamics for Transposable Elements

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)

TE documentation built on May 1, 2019, 10:13 p.m.