r2cluster: Write to Cluster file format

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):

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.

Examples

Run this code

#    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)

Run the code above in your browser using DataLab