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)