tetomonti

I realized that `.kstest`, as it is now implemented, does not match `ks.test`'s behavior when `alternative != "two.sided"`. In particular, the score in `ks.test` is defined as follows: STATISTIC

rctbl_build does not work with method="ks"

1

`rctbl_build` doesn't work at present when running ks test. It would be ideal to fix it and have it report, instead of the 'hits' (not relevant), the features in the...

It would be worthwhile to implement a version of the score similar to the one implemented in GSVA, where the difference between the top positive peak and the top negative...

Ideally, when hypeR is called with the KS test, the hypeR-dot plot should color-code the dots based on whether a geneset is positively (red) or negatively (blue) skewed (w/ white...

Vignettes are outdated?

2

This would be a great tool. Alas, most of the commands do not work as advertised in the vignettes. E.g., here's an example from the vignette "TCGAbiolinks: Downloading and preparing...

`ks_genescore_mat` --> `ks_rowscore` `wilcox_genescore_mat` --> `wilcox_rowscore` `revealer_genescore_mat` --> `revealer_rowscore`

Change `n_perms` to `n_perm` wherever it is used

Eliminate `ks_genescore` function after having properly implemented the plot function within it

Eliminate `topn_eval` function, and include a note in `cadra_search` indicating that it supersedes the former function

Add "number of permutations" to the cache key

1

Currently, the cache `key` for the permutation-based null distribution does not include the number of permutations `n_perm`. This should be included.