r2cluster: Write to Cluster file format

In ctc: Cluster and Tree Conversion.

Description

Converting data to Cluster format

Usage

r2cluster(data,labels=FALSE,colname="ACC",description=FALSE,
          file="cluster.txt",dec='.')

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 (ACC column in cluster file)
colname	a character string indicating what kind of objects are in each row. YORF, MCLID, CLID, ACC can be used: see details.
description	a logical value indicating whether we use the second column as description (NAME column for cluster file)
dec	the character used in the file for decimal points

Details

Software Cluster, made by M. Eisen needs formatted input data like:

ACC     NAME    GWEIGHT GORDER  V3      V4      V5
EWEIGHT                         1       1       1
gbk01   Gene1   1       1       0.9     0.4     1.4
gbk02   Gene2   1       2       0.6     0.2     0.2
gbk03   Gene3   1       3       1.6     1.1     0.9
gbk04   Gene4   1       4       0.4     1       1
  

First field of first line (i.e "ACC") is a special field, that tells program what kind of objects are in each row.

Four special values are defined with web link (when visualize with TreeView):

• YORF http://genome-www.stanford.edu/cgi-bin/dbrun/SacchDB?find+Locus+%22UNIQID%22

• MCLID http://genome.rtc.riken.go.jp/cgi-bin/getseq?g+R+UNIQID

• CLID http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceRes\-ult?op\-tion=CloneID&criteria1=IMAGE:UNIQID&choice=cDNA

• ACC http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceRes\-ult?op\-tion=Number&criteria=UNIQID&choice=cDNA

Line begining with EWEIGHT gives weights for each column (variable). Column GWEIGHT gives weights for each line (individuals).

Note

Cluster is a program made by M. Eisen that performs hierarchical clustering, K-means and SOM.

Cluster is copyrighted. To get or have information about Cluster: http://rana.lbl.gov/EisenSoftware.htm

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, r2xcluster, hclust

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

r2cluster(m)

ctc documentation built on Nov. 8, 2020, 5:11 p.m.