patternMarkers 'all' returning empty lists about cogaps

[dimalvovs]

related #78

[dimalvovs]

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)
})

[dimalvovs]

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))
})

[dimalvovs]

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

CoGAPS/R/methods-CogapsResult.R

Line 437 in cc8c42c

As <- sweep(As, 2, pscale, FUN="*")

are:

[1] 1363    7
[1] 9 7