r2xcluster: Write to Xcluster file format

Description Usage Arguments Details Note Author(s) References See Also Examples

View source: R/r2xcluster.R

Description

Converting data to Xcluster format

Usage

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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:

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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).

Note

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

Author(s)

Antoine Lucas, http://antoinelucas.free.fr/ctc

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

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##    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)

ctc documentation built on Nov. 17, 2017, 9:06 a.m.