phyloP.sph: phyloP SPH

Description

phyloP in SPH mode

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 is included with the subtree.

ref.idx

index of reference sequence in the alignment. If zero, use frame of reference of entire alignment. If -1 and features is used, try to guess the frame of reference for each feature based on sequence name.

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 computing a p-value of conservation, and the minimum is used when computing a p-value of acceleration. The variance of the posterior is computed exactly, but the confidence interval is based on the assumption that the combined distribution will be approximately normal (true for large numbers of sites by the central limit theorem).

quantiles

Logical. If TRUE, report quantiles of distribution rather than whole distribution.

Value

Either a list, data frame, or matrix, depending on options.