the commits in this PR contain the following changes:
add roxygen2 comments where missing so that all *.Rd files in ../man will be generated by roxygen2::roxygenise() instead of created and maintained manually (except ../man/GSVA-pkg-defunct.Rd which has to be kept to make R CMD check happy for the next release cycle.)
have the NAMESPACE file generated by roxygen2. This requires adding @import tags to R/AllClasses.R and a new file R/GSVA-package.R solely for this purpose.
with the old API now retired
replace remaining 'old' argument names by new ones in exported method signatures of filterGeneSets() and computeGeneSetsOverlap(), and
finally move coercion of matrices to dgCMatrix to top-level parameter object S4 methods (rather than doing it sometimes in functions for analysis methods)
resolves #122
the commits in this PR contain the following changes:
../manwill be generated byroxygen2::roxygenise()instead of created and maintained manually (except../man/GSVA-pkg-defunct.Rdwhich has to be kept to makeR CMD checkhappy for the next release cycle.)NAMESPACEfile generated by roxygen2. This requires adding@importtags toR/AllClasses.Rand a new fileR/GSVA-package.Rsolely for this purpose.filterGeneSets()andcomputeGeneSetsOverlap(), anddgCMatrixto top-level parameter object S4 methods (rather than doing it sometimes in functions for analysis methods)