reflect.phylo.hmm: Reflect a phylo-hmm across a strand
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Author(s) Examples

Reflect a phylo-hmm across a strand

1	reflect.phylo.hmm(x, pivot.states, mods = NULL)

`x`	An object of type hmm
`pivot.states`	The list of states to "reflect" across; these should be the states that are not strand-specific. Can be an integer vector containing state indices, or a character vector corresponding to state names (in `row.names(x$trans.mat)`)
`mods`	A list of objects of type `tm` representing phylogenetic models corresponding to each state in the hmm. If given, then the models will also be reflected and the return value will be a list with a new hmm and a new list of models.

If mods==NULL then a new hmm will be returned. Otherwise a list containing the new hmm and the corresponding models will be returned.

Melissa J. Hubisz and Adam Siepel

#state.names <- c("neutral", "conserved", "codon1", "codon2", "codon3")
#h <- hmm(t(matrix(c(0.95, 0.04, 0.01, 0, 0, 
#                    0.04, 0.95, 0.01, 0, 0,
#                    0,    0,    0,    1, 0,
#                    0,    0,    0,    0, 1,
#                    0.005, 0.005,  0.99,   0, 0), nrow=5,
#                  dimnames=list(state.names, state.names))))
#         eq.freq=c(0.6, 0.3, 0.1/3, 0.1/3, 0.1/3))
#reflect.phylo.hmm(h, c("neutral", "conserved"))