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NKI-CCB / DISCOVER

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
Apache License 2.0
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Important Documentation Missing #10

Closed DarioS closed 4 years ago

DarioS commented 4 years ago

The software is described as

DISCOVER is a novel statistical test for detecting co-occurrence and mutual exclusivity in cancer genomics data.

but the vignette doesn't have any example of how to test for co-occurrence

We can now test for mutual exclusivity between all pairs of genes ...

Can DISCOVER R package do a test for co-occurrence?

Also, the functions lack any documentation.

No man pages found in package ‘discover’

Lastly, I think it would also be beneficial to many readers to have an example of converting a MAF file obtained from Genomic Data Commons into the matrix used rather than just data("BRCA.mut").

scanisius commented 4 years ago

Thank you for reporting this issue. Unfortunately, the function-level documentation has not been included in the DISCOVER distribution packages, even though it is present in the R source files. I will fix this and also extend the vignette.

In the meantime, let me explain to you how to use the co-occurrence test. The pairwise.discover.test function takes an optional argument called alternative. If its value is "less" (the default), a mutual exclusivity test is performed. If its value is "greater", a co-occurrence test is performed.

scanisius commented 4 years ago

The latest version of the DISCOVER R package (0.9.3) now includes function-level help pages. These can be accessed using R's standard ? syntax, e.g. ?pairwise.discover.test.