interface {scaleboot}R Documentation

Interface to External Packages

Description

Interface for other packages such as CONSEL (phylogenetic inference), and pvclust (hierarchical clustering)

Usage

read.mt(file,tlab="t")

read.ass(file,identity=TRUE,tlab="t",elab="e") 

read.cnt(file)

## S3 method for class 'pvclust':
sbfit(x,...)

sbpvclust(x,mbs,k=3,select="average",...)

Arguments

file character of a file name to be read.
identity logical. Should the identity association be included?
tlab character for basename of tree labels.
elab character for basename of edge labels.
x an object of class "pvclust".
mbs an object of class "scalebootv".
k numeric of k for a AU p-value.
select character of model name (such as "poly.3") or one of "average" and "best".
... further arguments passed to or from other methods.

Details

CONSEL is a program package consisting of small programs written in the C language for assessing the confidence of phylogenetic tree selection. Some functions for interfacing with CONSEL are: read.mt, read.ass, and read.cnt for reading, respectively, mt, ass, and cnt format. Once mt file is read, we can calculate improved versions of approximately unbiased p-values by relltestin scaleboot instead of CONSEL.

pvclust is a R package for hierarchical clustering with p-values. Functions for interface to pvclust are: sbfit method for an object of class "pvclust" to convert it to "scalebootv" class, and sbpvclust for writing back the result to a "pvclust" object.

Value

read.mt returns a matrix of dimension sequence-length by tree-number. If identity=FALSE, then read.ass returns a list containing components x for edge->tree associations and y for tree$to$edge associations. If identity=TRUE, read.ass returns a list vector of edge$to$tree associations, where the identity associations for tree$to$tree are included. read.cnt returns a list containing components bps, nb, and sa to be used for sbfit. The list also contains components cnt, id, and val.
sbfit.pvclust returns an object of class "scalebootv". sbpvclust returns an object of class "pvclust".

Author(s)

Hidetoshi Shimodaira

References

Shimodaira, H. and Hasegawa, M. (2001). CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246-1247 (software is available from http://www.is.titech.ac.jp/~shimo/prog/consel/).

Suzuki, R. and Shimodaira, H. (2006). pvclust: An R package for hierarchical clustering with p-values, Bioinformatics, 22, 1540-1542 (software is available from CRAN or http://www.is.titech.ac.jp/~shimo/prog/pvclust/).

See Also

relltest

Examples


## Not run: 
## reading CONSEL files
## sample files are found in mam15 subdirectory
## see help(mam15) for details
mam15.mt <- read.mt("mam15.mt")
mam15.ass <- read.mt("mam15.ass")
mam15.cnt <- read.mt("mam15.cnt")
## End(Not run)

## Not run: 
## see help(lung73) for details
data(lung73)
lung73.sb <- sbfit(lung73.pvclust,cluster=cl) # model fitting
lung73.new <- sbpvclust(lung73.pvclust,lung73.sb) # au <- k.3
## End(Not run)


[Package scaleboot version 0.3-2 Index]