[BioC] cosine similarity

joe j joe.stata at gmail.com
Mon Jun 27 17:34:54 CEST 2011

Thanks a lot Achilleas, Kevin,

Kevin, "distanceMatrix" funciton works great, although distance is
calculated across columns-but I guess a simple transpose would do the

I compared the result (for two rows) with the function written by
Achilleas. They seem to be identical except that one is distance, the
other is correlation.

Thanks very much, again!

On Mon, Jun 27, 2011 at 4:27 PM, Kevin R. Coombes
<kevin.r.coombes at gmail.com> wrote:
> Check the "distanceMatrix" funciton in the "ClassDiscovery" package that is
> part of OOMPA.
> R repository located at
>    http://bioinformatics.mdanderson.org/OOMPA
> Instructions for installation and some documentation at
>    http://bioinformatics.mdanderson.org/Software/OOMPA
>  -- Kevin
> On 6/27/2011 7:24 AM, joe j wrote:
>> Dear All,
>> I am after a package that would calculate the uncentred correlation
>> (or cosine similarity; http://en.wikipedia.org/wiki/Cosine_similarity)
>> between pairs of observations. I know that bioconductor has packages
>> that compute distance measures such as mahalanobis distance (the
>> package mdqc does this). Is there any package that calculates cosine
>> similarity?
>> Regards,
>> Joe.
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