My question regards how the odds ratios are calculated for somatic mutations in cBioPortal.
Which kinds of mutations are included in the calculations? Specifically, are silent mutations included in the odds ratio?
Secondly, are the somatic mutations collected from each tumor sample —with possibly multiple tumor samples per patient — or from only one sample per patient?
If there is any other preprocessing involved with somatic mutations could you please let me know.
1 answer
The odds ratio are calculated based on the query performed, so it's using the same data as in the Oncoprint tab. Only non-silent mutations are currently supported in cBioPortal. Most of the patients in cBioPortal, especially TCGA, have only one sample. Some studies contains patients with multiple samples and we are seeing such cases more and more. The mutual exclusivity calculation is always based on samples.
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Something about computing methods which are used in cBioPortal are described in the publication: Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal (it is available from cBioPortal home page). You will find some information there.