[BioC] Importing .cdt files generated by Cluster3.0 into R

[Kevin R. Coombes]

Actually, it's a little trickier than that, since you would really like 
to read things into R in a manner that constructs objects that R will 
recognize and plot as a dendrogram (or an "hclust" object) as part of a 
heatmap.  I have attached an R script that does this.  It assumes that 
you have a set of three files with names of the form
     x.cdt
     x.gtr
     x.atr
and reads them into a list with three components:
     data    (a matrix)
     gene    (an hclust)
     arry    (an hclust)
It's not terribly robust, and it assumes that the files were generated 
using the default settings from Mike Eisen's cluster and treeview 
programs. But it is heavily commented, so you might be able to modify it 
to do what you want if it doesn't work out of the box.

Best,
     Kevin

On 10/18/2011 2:26 PM, Valerie Obenchain wrote:
> Hello,
>
> For importing these files into R see ?read.table and ?read.delim.
>
> Reading the gtr should be fairly straightforward with read.table. The 
> cdt file might be better with read.delim and set fill=TRUE.
>
> Valerie
>
>
>
> On 10/18/2011 07:58 AM, Sohail [guest] wrote:
>> Dear All,
>>
>> I have used the Cluster3.0 to generate cluster for gene expression 
>> data.  I would like to import these files (.cdt,.gtr) into R. to 
>> generate silohuette plots.
>> Basically, I would like to check for the robustness of the clusters.  
>> Could the files from Cluster3.0 be imported into R?  I would 
>> appreciate any other suggestions.
>> Thanks.
>>
>>   -- output of sessionInfo():
>>
>> none
>>
>> -- 
>> Sent via the guest posting facility at bioconductor.org.
>>
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