amap (version 0.5-1)

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='.')

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):

• YORFhttp://genome-www.stanford.edu/cgi-bin/dbrun/SacchDB?find+Locus+%22UNIQID%22
• MCLIDhttp://genome.rtc.riken.go.jp/cgi-bin/getseq?g+R+UNIQID
• CLIDhttp://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceRes-ult?op-tion=CloneID&criteria1=IMAGE:UNIQID&choice=cDNA
• ACChttp://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).

See Also

xcluster, r2xcluster, hclust

Examples

#    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

r2cluster(m)