Question: Package in R to determine which factor values are overrepresented within a particular factor of interest
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gravatar for IOM
3.1 years ago by
IOM20
Birmingham
IOM20 wrote:

Hi,

Thanks for reading. I have performed some clustering using copy number data from SNP arrays. I would like to know if those clusters are enriched for any of the clinical data/factors the samples come with. One example of a result for cluster 1 could be:

Enrichment

Cluster 1 (36)

         

Factor

Factor Value

No. in Factor Group

No. in Selected Samples

% in Factor Group

% in Selected Samples

P-Value

Recurrence

Yes

11

12

30.56

12.24

4.74E-05

Multifocal

Yes

17

27

47.22

27.55

0.00112141

This table would show only the first two lines of the results for the 1st cluster (it would have more), that contains 36 samples (every cluster would have a table like this). From all the samples selected (all samples from all clusters), 12 have YES as factor value for RECURRENCE factor. From this 12 samples, 11 belong to cluster 1, so it has a significant p-value meaning that this group would be enriched for RECURRENCE. The same would be for MULTIFOCAL.

I have made several searches for a package that performs this, but results always are related to transcription factor enrichment. Please, does anyone know any? Any help would be much appreciated. Thanks

Regards

 

IOM 

ADD COMMENTlink written 3.1 years ago by IOM20
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