phyloP.prior: phyloP prior
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Examples

Prior distribution on number of substitutions

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phyloP.prior(mod, nsites = 100, subtree = NULL, branches = NULL,
  outfile = NULL, outfile.only = FALSE, quantiles = FALSE,
  epsilon = 1e-10)

`mod`	An object of class `tm` representing the neutral model.
`nsites`	The number of sites in the alignment
`subtree`	Character string specifying the name of a node in the tree. If given, partition the tree into the subtree beneath the node and the complementary supertree, and compute joint number of substitutions in the sub/supertree. The branch above the specified node is included in the subtree.
`branches`	A vector of character strings givingi the names of branches to consider in the subtree. The remaininig branches are in the supertree. Return joint distribution of number of substitutions in sub/supertree.
`outfile`	Character string. If given, write results to given file.
`outfile.only`	Logical. If `TRUE`, do not return any results to R (this may be useful if results are very large).
`quantiles`	Logical. If `TRUE`, report quantiles of distribution rather than whole distribution.
`epsilon`	Numeric value indicating the thhreshold used in truncating tails of distributions; tail probabilities less than this value are discarded. This only applies to the right tail.

A data.frame. If quantiles=FALSE, the columns will be the number of substitutions and their probability under the null model. If quantiles=TRUE, there will be 101 rows with the 0, 0.05, ..., 1.0th quantile.

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")