New functionalities for transformation and test functions

[LotharukpongJS]

Updated myTAI (to version 1.0.1.000) with some fixes and some new functionalities.

Transformations

• Updates to tf() function, which transforms expression data:
  • Variance stabilising transformations from DESeq2, i.e. rlog and vst, can now be implemented. The new intergerise parameter (default is FALSE) should be set to TRUE when integers are demanded for the user's transformation of choice such as in rlog and vst.
  • Pseudocount, i.e. log2(x+pseudocount), can be implemented through the new pseudocount parameter.
  • Added documentation for performing rank transformation, which assigns ranks to the gene expression values within each stage, based on their relative positions compared to other values.
• New tfStability() function to test the robustness of the p-values of a given test (e.g. FlatLineTest(), ReductiveHourglassTest(), ReverseHourglassTest(), EarlyConservationTest() and LateConservationTest()) to expression data transformations. This new function essentially wraps around the test functions and the tf() functions.

Phylotranscriptomic pattern tests

• New LateConservationTest() and lcScore() functions to test for a high-mid-low (or high-high-low) TAI or TDI pattern. This is built upon the code for the EarlyConservationTest() and the ecScore().
• Improvements to existing test functions (ecScore(), rhScore() and reversehourglassScore()) to give a message when the phylotranscriptomic pattern is unlikely to follow the test statistics.

Fixes

• A few lines of code have been changed where appropriate to remove errors and warnings from devtools::test() and devtools::check().

Unit tests for the above-mentioned changes have been updated where appropriate. The new package passes the unit tests via devtools::test() and is checked using all known best practices via devtools::check().

[HajkD]

Dear @LotharukpongJS

Beautiful work!!! Thank you so much for pushing this forward!

I particularly like the new later conservation test function and transformation functions!

Feel free to send me another pull request where you place all your new updates into the NEWS.md file for the next myTAI version release.

With very best wishes!