dimalvovs
dimalvovs
@kwoyshner can you review please?
@kwoyshner do you want to have a look at `threshold = 'cut'`? I've updated it too. This part of code is poorly documented so I was not sure what that...
The checkpoints are disabled by default: ``` > > library("CoGAPS") > packageVersion("CoGAPS") [1] ‘3.24.0’ > CoGAPS::checkpointsEnabled() [1] FALSE ``` It looks like these are disabled in https://github.com/FertigLab/CoGAPS/blob/cc8c42cd2a9dc9c99e63e22dba076fabfdb8461e/configure#L3241 Potentially could be...
Related to #49
original patternMarkers version for inspiration ``` #' patternMarkers #' #' @param Amatrix A matrix of genes by weights resulting from CoGAPS or other NMF decomposition #' @param scaledPmatrix logical indicating...
the results between the current (#102) patternMarkers and the original has diverted: ``` data(GIST) res pm_current_cut pm_orig_cut lengths(pm_current_cut$PatternMarkers) Pattern_1 Pattern_2 Pattern_3 Pattern_4 Pattern_5 Pattern_6 Pattern_7 14 46 10 270 27...
related https://github.com/FertigLab/CoGAPS/pull/78
confirmed warning in `threshold = "cut"` ``` test_that("patternMarkers work with threshold = 'cut' yields no warning", { #set up data(GIST) res
confirmed empty markers with `threshold = 'all'` ``` test_that("patternMarkers work with threshold = 'all' for general mode", { #set up data(GIST) res
the problem with warnings generated in case of `threshold='cut'` comes from the non-matching dimensions of As and Ps during the scaling and `sweep`ing . For the testdata trained on nPatterns=7,...