FertigLab
patternMarkers 'all' returning empty lists
Hi! I am trying to obtain patternMarkers from a cogaps result object using the following code: pMarks <- patternMarkers(NMF, threshold = "all", lp = NA, axis = 1)
It returns values for the scores and ranks how I would expect, but there are no patternMarkers for every pattern -- which seems weird.
The 'cut' version does return patternMarkers, but the output is formatted slightly differently than that returned by 'all' (each list isn't named by the pattern name), and there is a warning message I haven't seen before when using this function.
I am using R 4.3.0 and CoGAPS 3.24.0 (installed 5/2/24). I have never run into this issue before, but I had just reinstalled CoGAPS.
Looking into the patternMarkers code here (lines 480-490):
If I print the first few elements of thresholdTest it looks like a named list, but if I print the gene followed by names(gene) for each, the names are NULL
I'm not sure if this is happening for anyone else. Please let me know if you need any other details!
confirmed warning in threshold = "cut"
test_that("patternMarkers work with threshold = 'cut' yields no warning", {
#set up
data(GIST)
res <- CoGAPS(GIST.data_frame, nIterations=1000,
seed=1, messages=FALSE)
test <- patternMarkers(res, threshold = "cut")
expect_no_warning(length(test$PatternMarkers), 0)
})
confirmed empty markers with threshold = 'all'
test_that("patternMarkers work with threshold = 'all' for general mode", {
#set up
data(GIST)
res <- CoGAPS(GIST.data_frame, nIterations=1000,
seed=1, messages=FALSE)
test <- patternMarkers(res, threshold = "all")
marker_lengths <- sapply(test$PatternMarkers, length)
expect_equal(sum(marker_lengths > 0), length(marker_lengths))
})
the problem with warnings generated in case of threshold='cut' comes from the non-matching dimensions of As and Ps during the scaling and sweeping . For the testdata trained on nPatterns=7, the dimensions of A and P that are fed into here https://github.com/FertigLab/CoGAPS/blob/cc8c42cd2a9dc9c99e63e22dba076fabfdb8461e/R/methods-CogapsResult.R#L437 are:
[1] 1363 7
[1] 9 7