inst/examples/phastCons.R

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
files <- c("ENr334-100k.fa", "rev.mod")
unzip(exampleArchive, files)
mod <- read.tm("rev.mod")
msa <- read.msa("ENr334-100k.fa")
rv <- phastCons(msa, mod)
names(rv)
rv2 <- phastCons(msa, mod, estimate.trees=TRUE)
names(rv2)
rv2$tree.models
unlink(files)

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rphast documentation built on May 30, 2017, 5:13 a.m.