Support for combining scores from directional gene sets

[rcastelo]

Following up this conversation at the Bioconductor support site, consider adding support to combine scores from directional gene sets.

[rocanja]

I often work with pairs of directional gene sets where gene set 'A' represents genes upregulated by a stimulus or a particular condition and gene set 'B' contains the respective downregulated genes. Scoring them separately is important for the biological interpretation, but (mainly) for visualisation it would be very helpful to be able to summarise the two scores into a combined score that represents the 'concordance' with the respective condition or 'phenotype' that is decribed by the gene set pair. In the {singscore} package something conceptually similar is realised by deriving a 'Total Score'. It would be great if something along those lines could be considered for implementation into the {GSVA} package in a future release. Mathematically, maybe A+(-1*B) would be a suitable approach, but happy to leave this decision to people with a stronger mathematical background.

[rcastelo]

Hi! glad to see you here contributing. Thanks for the explanation. Do you know of any paper where this approach has been used for visualization or other analytical purposes?