CoGAPS
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FertigLab
Bayesian MCMC matrix factorization algorithm
From the vignette + documentation, it's not entirely clear to me what the difference between distributed = "genome-wide" and distributed = "single-cell" is. What is changing? I note that for...
When CoGAPS is run in distributed mode, one of the matrix gets fixed, thus making standard deviation absent from the output. Lets think of ways to being it back.
Good afternoon! I recently ran into an issue where there is pattern discrepancy between runs with sparseOptimization set to TRUE versus FALSE. The code I ran and the output is...
There are tests in the https://github.com/FertigLab/CoGAPS/tree/master/src/cpp_tests, but we seem to have lost the knowledge of how up to date those are and do those work at all. Are the tests...
Here is a comment left by someone [in the code](https://vscode.dev/github/FertigLab/CoGAPS/blob/master/R/class-CogapsResult.R#L80-L81), let's treat it properly here. ``` # TODO: fix this check for semisupervised case # if (sum(object@featureLoadings < 0) >...
As my 3-hour CoGAPS run finished up, the following error appeared: ``` Matching Patterns Across Subsets... Error in corcut(allPatterns, gapsParams@cut, gapsParams@minNS) : NA values in correlation of patterns In addition:...
It would be nice if CoGAPS could read data directly from an hdf5 (particularly h5ad) file.
The most recent Version 3.18.0 fails to install on my computer. Version 3.15.2 installs correctly. I think this may be due to a C++ compiling error on Mac with M1...
Good afternoon! I recently have run into large changes in the atoms (A) and (P) matrix values when running CoGAPS across multiple nSets. In a previous issue, these numbers were...
