Updates to `Discussing Genomic Phylostratigraphy` and `Introduction to the myTAI package`

[LotharukpongJS]

I have updated the Discussing Genomic Phylostratigraphy and Introduction to the myTAI package articles as well as the README. Improvements include a spell-check, updates to the genomic phylostratigraphy debate and tools that can be used. There are of course more aspects to these debates but I think we have a good summary.

One interesting point I haven't touched on is the difference between using deep sequence homologues (i.e. phylogenetically deepest hit using pairwise sequence aligners or perhaps now also structural aligners) vs orthogroups (i.e. group of genes descended from a single gene in the last common ancestor of a clade of species).

Some aspects of this debate will be added to Discussing Genomic Phylostratigraphy since several studies differ in these approaches and I will do a spell check on the other vignettes.

[LotharukpongJS]

I have now added a section on Inferring gene age using orthogroups to the article Discussing Genomic Phylostratigraphy.

[LotharukpongJS]

I have now skimmed through the spelling and made the appropriate changes. Once all the speed-ups and fixes from @lavakin have been implemented, we might want to rebuild the entire site again with pkgdown::build_site() and change the number of permutations (i.e. =20000) in the function example so that users know that many permutations can be used.

I haven't rebuilt the site yet in this pull request. But for example, some reference vignettes don't look so nice due to excessive printouts.

E.g. CombinatorialSignificance().

In the function example, the number of permutations is specified originally as 10 (presumably for speed). But the print-out of

We recommended using at least 20000 permutations to achieve a sufficient permutation test.

doesn't make the reference page for the CombinatorialSignificance() function look so nice in its current form.

p.vector <- CombinatorialSignificance(ExpressionSet = PhyloExpressionSetExample, 
                                      replicates    = c(2,3,2), 
                                      TestStatistic = "FlatLineTest", 
                                      permutations  = 10, 
                                      parallel      = FALSE)
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#>

Anyway, I hope you all have a nice start to the week!

[HajkD]

Dear @LotharukpongJS

I absolutely love your discussion on orthogroups! Very well done!

I hope we can also get some external feedback to further stimulate this discussion and keep it as scientifically balanced as possible.

With many thanks, Hajk