| r2xcluster {ctc} | R Documentation |
Converting data to Xcluster format
r2xcluster(data,labels=FALSE,description=FALSE,file="xcluster.txt")
file |
the path of the file |
data |
a matrix (or data frame) which provides the data to put into the file |
labels |
a logical value indicating whether we use the frist column as labels (NAME column for xcluster file) |
description |
a logical value indicating whether we use the second column as description (DESCRIPTION column for cluster file) |
Software Xcluster, made by G. Sherlock needs formatted input data like:
NAME DESCRIPTION GWEIGHT V2 V3 V4 EWEIGHT 1 1 1 gbk01 Gene1 1 0.9 0.4 1.4 gbk02 Gene2 1 0.6 0.2 0.2 gbk03 Gene3 1 1.6 1.1 0.9 gbk04 Gene4 1 0.4 1 1
Line begining with EWEIGHT gives weights for each
column (variable). Column GWEIGHT gives weights for each line
(individuals).
Xcluster is a C program made by Gavin Sherlock that performs hierarchical clustering, K-means and SOM.
Xcluster is copyrighted. To get or have information about Xcluster: http://genome-www.stanford.edu/~sherlock/cluster.html
Antoine Lucas, http://antoinelucas.free.fr/ctc
xcluster, xcluster2r, hclust, hcluster
## Create data
.Random.seed <- c(1, 416884367 ,1051235439)
m <- matrix(rep(1,3*24),ncol=3)
m[9:16,3] <- 3 ; m[17:24,] <- 3 #create 3 groups
m <- m+rnorm(24*3,0,0.5) #add noise
m <- floor(10*m)/10 #just one digits
r2xcluster(m)
## And once you have Xcluster program:
## Not run:
system('Xcluster -f xcluster.txt -e 0 -p 0 -s 0 -l 0')
h <- xcluster2r('xcluster.gtr')
plot(h,hang=-1)
## End(Not run)