ctc (version 1.46.0)

r2xcluster: Write to Xcluster file format

Description

Converting data to Xcluster format

Usage

r2xcluster(data,labels=FALSE,description=FALSE,file="xcluster.txt")

Arguments

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)

Details

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).

References

Antoine Lucas and Sylvain Jasson, Using amap and ctc Packages for Huge Clustering, R News, 2006, vol 6, issue 5 pages 58-60.

See Also

xcluster, xcluster2r, hclust, hcluster

Examples

##    Create data
set.seed(1)
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)