Re: [R] Partition data into clusters

2008-03-24 Thread Suhaila Zainudin 
Hi,

Thanks for your reply. I have tried yr suggestions with success. TQVM.

I have another query, say I want to write each cluster into a csv file such
as follows:

clus1 - my.clusters[[1]]
write.csv(clus1, file = clus1.csv)

.
.
clus10 - my.clusters[[10]]
write.csv(clus10,file = clus10.csv)

I can write the functions to do that for all 10 clusters by repeatedly
calling write.csv as  above. Is there a more elegant way of doing it by
using a loop (for example).

for(i in 1:xx) {
clusn - my.clusters[[n]]
write.csv(clusn, file = clusn.csv)
}

I am trying something using list as well, as folows:

names( my.clusters ) - paste('Cluster_',1:10, sep='')

Now I can  use

my.clusters$Cluster_1

The above will return all members of Cluster_1.

I have an idea to use lapply or sapply to do write.csv on each
components(Cluster_1.Cluster_n)  from my.clusters, that will do the same
as the loop example. Maybe this is the better way..


Any comments are appreciated.

Thanks!

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Re: [R] Partition data into clusters

2008-03-24 Thread Suhaila Zainudin 
Hi,

Just to inform you that I found the solution for the write.csv  task I
mentioned earlier. Searching thru the r-help leads me to this solution..

###Your soln starts
xx  - max(cl2$cl.kmr10.cluster)
# find out how many clusters there are.
my.clusters - list(NULL)  # set up an empty list for storage

#  Loop through the dataset and subset by cluster.
for(i in 1:xx) {
 my.clusters[[i]] - subset(cl2,
cl2$cl.kmr10.cluster==i)
 }
# Eh voilà!
my.clusters


### Your solution ends

# Soln for writing the clustered results into multiple files using loop.


for(i in 1:xx) {
  write.csv(my.clusters[[i]], paste(mycluster,i,sep=.))
}



Regards

suhaila

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Re: [R] Partition data into clusters

2008-03-19 Thread John Kane 
Can you supply a small self-contained example of this?
--- Suhaila Zainudin [EMAIL PROTECTED]
wrote:

 Greetings R-users,
 
 I have been using the fpc package in R to cluster my
 data. Speficically I am
 using kmeansruns clustering.
 I would like to know how I use R to partition data
 into clusters. What I am
 doing is as follows.
 
 # Use csv file as input
 #
 wholeset = read.csv(Spellman800genesImputed.csv)
 
 # exclude first col (gene names)
 ##
 wholeset2 = wholeset[,-1]
 
 #Use fpc
 ###
 library(fpc)
 
 cl.kmr10 - kmeansruns(wholeset2,k=10,runs=10)
 
 
 #append cluster label to original dataset
 ###
 cl2 - data.frame(wholeset, cl.kmr10$cluster)
 
 After this step, I write cl2 into a csv file and
 manually partition data
 into its respective clusters using Excel.
 Then I read the data from each clusters back into R
 for further analysis.
 
 Can I do the data partitioning directly in R?
 
 TQ
 
 
 -- 
 Suhaila Zainudin
 PhD Candidate
 Universiti Teknologi Malaysia
 
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