This PR resolves #121 by replacing the internal function .gsva_newAPI() with genuine gsva() S4 methods for parameter objects (temporarily the new API had been implemented by dispatching to S4 methods only to call the same internal function).
Also there are now methods for wrapping (or rather, coercing) the results from sparse matrices passed as dgCMatrix objects, in an effort to make the return datatype match the input datatype.
In addition, existing unit tests (with the temporary exception of DelayedMatrix) have been modified to make use of the new gsva() API as the penultimate step to porting package-internal code (the final step will be the Shiny app in igsva()) before making the now deprecated old API defunct.
This PR resolves #121 by replacing the internal function
.gsva_newAPI()with genuinegsva()S4 methods for parameter objects (temporarily the new API had been implemented by dispatching to S4 methods only to call the same internal function).Also there are now methods for wrapping (or rather, coercing) the results from sparse matrices passed as
dgCMatrixobjects, in an effort to make the return datatype match the input datatype.In addition, existing unit tests (with the temporary exception of
DelayedMatrix) have been modified to make use of the newgsva()API as the penultimate step to porting package-internal code (the final step will be the Shiny app inigsva()) before making the now deprecated old API defunct.