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,select="average",...)
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. |
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 relltest
in
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)