Nothing
suppressMessages(library(cubfits, quietly = TRUE))
set.seed(1234)
# Normalize phi.Obs
phi.Obs <- ex.train$phi.Obs / mean(ex.train$phi.Obs)
# Generate sequences.
da.roc <- simu.orf(length(phi.Obs), b.Init$roc,
phi.Obs = phi.Obs, model = "roc")
names(da.roc) <- names(phi.Obs)
write.seq(da.roc, "toy_roc.fasta")
# Read seqeuences back.
seq.roc <- read.seq("toy_roc.fasta")
seqstring.roc <- convert.seq.data.to.string(seq.roc)
phi <- data.frame(ORF = names(phi.Obs), phi.value = phi.Obs)
# Generate data structures from sequences.
aa.names <- names(b.Init$roc)
reu13.df <- gen.reu13.df(seqstring.roc, phi, aa.names = aa.names)
n <- gen.n(seqstring.roc, aa.names = aa.names)
y <- gen.y(seqstring.roc, aa.names = aa.names)
# Run codon fits.
.CF.AC$renew.iter <- 3
ret.time <- system.time({
ret <- cubfits(reu13.df, ex.train$phi.Obs, y, n,
nIter = 20,
verbose = TRUE, report = 5,
model = "roc", adaptive = "simple")
})
x <- rowMeans(do.call("cbind", ret$phi.Mat)[, 11:20])
y <- ex.train$phi.Obs
plotprxy(x, y)
x <- log10(x / mean(x))
y <- log10(y / mean(y))
print(mean(x))
print(summary(lm(y ~ x))$r.squared)
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