NEWS

RNentropy 1.3.3

RN_iso_calc and RNentropy_iso_switch no longer return res, which duplicated gene_status and pv.
The default gene-level threshold of RN_iso_select (gene_pv) is now 0.05 (previously 0.01).
Corrected the package citation, which now lists the 2018 Nucleic Acids Research article and the 2021 Methods in Molecular Biology chapter.
Corrected and completed several help pages: an overview of both analyses in the package help, the exact testability rule of min_expr, cross-references between the isoform-switch functions, fixes to the dataset descriptions, and removal of outdated copies of the source code from the examples.

RN_iso_select now combines the sample p-values of each TESTED gene into a gene-level p-value with the Simes method and compares it with the threshold, without correction across genes. The threshold argument lpv_t is renamed gene_pv, the method argument and the lpv_adj component are removed, and the gene-level p-values are returned as gene_pv. selected reports the gene-level p-value (ISO_GENE_PV) next to the uncorrected per-sample p-values.
RN_iso_calc and RNentropy_iso_switch return the per-sample p-values as pv (formerly lpv), with columns named ISO_PV_<sample> (formerly ISO_LPV_<sample>).
Renamed the sample columns of RN_IsoSwitch_Example_S7 and of the compact S7 example file to plain tissue names (brain, heart, kidney, liver, lung, muscle).

Added RN_iso_select to apply multiple-testing correction to isoform-switch local p-values and retain genes significant in at least one sample.
Added runnable file-based examples for the standard and isoform-switch workflows using a shared synthetic regression dataset.

Initialized the public GitHub development repository from the verified CRAN 1.2.3 release.
Added continuous integration and repository provenance metadata.
Added RN_iso_calc and RNentropy_iso_switch for the analysis of isoform switching, with explicit testability information and results validated against the independent C++ implementation.
Added the complete historical S7 isoform-switch example as the compressed RN_IsoSwitch_Example_S7 package dataset.