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102 patternmarkers all returning empty lists #103

Merged
merged 31 commits into from
Jun 5, 2024
Merged

102 patternmarkers all returning empty lists #103

merged 31 commits into from
Jun 5, 2024

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dimalvovs
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  • add a test that fails on empty patterMarkers
  • make it pass by rewriting the method for threshold='all'

@dimalvovs dimalvovs linked an issue May 2, 2024 that may be closed by this pull request
patternMarkers 'all' returning empty lists #102
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@dimalvovs
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@kwoyshner can you review please?

@kwoyshner
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I tried reinstalling from this branch and was able to get patternMarkers with 'all' now, thank you!

@dimalvovs
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@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 mode should do but there was a dimension mismatch. simplicityGENES function needs to be inspected for functionality.

@dimalvovs dimalvovs marked this pull request as ready for review May 5, 2024 22:50
jmitchell81
jmitchell81 approved these changes May 8, 2024
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drbergman
drbergman reviewed May 8, 2024
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I am unqualified to comment on how these changes affect the integrity of the CoGAPS algorithm, but I left a few comments. Hopefully, it helps in some small way!

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tests/testthat/test_output_across_modes.R Outdated Show resolved Hide resolved
@dimalvovs dimalvovs requested a review from genesofeve May 9, 2024 21:30
genesofeve
genesofeve reviewed May 29, 2024
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please reinstate

@dimalvovs dimalvovs merged commit 45fdd42 into master Jun 5, 2024
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@dimalvovs dimalvovs deleted the 102-patternmarkers-all-returning-empty-lists branch June 5, 2024 19:28
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@drbergman drbergman drbergman left review comments

@genesofeve genesofeve genesofeve left review comments

@jmitchell81 jmitchell81 jmitchell81 approved these changes

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patternMarkers 'all' returning empty lists
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@dimalvovs @kwoyshner @genesofeve @drbergman @jmitchell81