Usage
phyloP.sph(mod, msa=NULL, mode="CON", features=NULL, basewise=FALSE,
subtree=NULL, ref.idx=1, outfile=NULL, outfile.only=FALSE,
outfile.format="default", prior.only=FALSE, nsites=NULL,
post.only=FALSE, fit.model=FALSE, epsilon=ifelse(basewise, 1e-06,
1e-10), confidence.interval=NULL, quantiles=FALSE)Arguments
mod
An object of class tm representing the neutral model.
msa
The multiple alignment to be scored.
mode
The type of p-value to compute. One of "CON", "ACC",
"NNEUT", or "CONACC".
features
A features object of type feat. If given, compute
p-values for each element.
basewise
Logical. If TRUE, compute scores for every base
in reference sequence. Cannot be TRUE if features is provided.
subtree
A character string giving the name of a node in the tree.
Partition the tree into the subtree beneath the node and the
complementary supertree, and consider conservation/acceleration in the
subtree given the supertree. The branch above the specified node
ref.idx
index of reference sequence in the alignment. If zero,
use frame of reference of entire alignment.
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 for saving memory).
outfile.format
Character string describing output format. Possible
formats depend on other options (see description below).
prior.only
Logical. If TRUE, compute only prior
distribution of number of substitutions over nsites sites. Alignment
is ignored in this case.
nsites
Integer. Number of sites to consider if prior.only is
TRUE.
post.only
Logical. If TRUE, compute the posterior
distribution of the number of substitutions given the the neutral model
and the alignment.
fit.model
Logical. If TRUE, re-scale the model (including
a separate scale for the subtree, if applicable) before computing the
posterior distribution. This makes p-values less conservative.
Cannot currently be used with features.
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.
confidence.interval
Numeric value between 0 and 1. If given,
allow for uncertainty in the estimate of the actual number of substitutions
by using a central confidence interval about the mean of given size.
To be conservative, the maximum of this interval is used when comput
quantiles
Logical. If TRUE, report quantiles of distribution
rather than whole distribution.