inst/examples/phyloP-prior.R

In rphast: Interface to 'PHAST' Software for Comparative Genomics

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
unzip(exampleArchive, "rev.mod")
tm <- read.tm("rev.mod")
t1 <- phyloP.prior(tm, nsites=10)
t2 <- phyloP.prior(tm, nsites=20)
t3 <- phyloP.prior(tm, nsites=20, quantiles=TRUE)
t4 <- phyloP.prior(tm, nsites=20, epsilon=1e-20)
plot(t1$nsub, t1$prior)
points(t2$nsub, t2$prior, col="red")
unlink("rev.mod")