| interface {scaleboot} | R Documentation |
Interface for other packages such as CONSEL (phylogenetic inference), and pvclust (hierarchical clustering)
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,k.bp=1,...)
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". |
... |
further arguments passed to or from other methods. |
k |
numeric of k for a AU p-value. |
k.bp |
numeric of k for a BP p-value. |
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.
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".
Hidetoshi Shimodaira
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/).
## 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)