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uclahs-cds / package-iSubGen

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README example code bugs #11

Open jarbet opened 3 weeks ago

jarbet commented 3 weeks ago

In this example, csnvs should be snv

In this example I get an error, could be related to the new matrix checks in #5

Error in "matrix" != class(data.matrix) && "data.frame" != class(data.matrix) : 'length = 2' in coercion to 'logical(1)'

I recommend double checking that the rest of the examples work after fixing the above 2 bugs

maotian06 commented 3 weeks ago

Thanks for catching that @jarbet !!!

The first issue is a typo and will be fixed in PR #9

The second issue is due to the current class(molecular.data$cna) would return 2 vectors instead of one: "matrix", "array". I will try to fix that in #5

maotian06 commented 2 weeks ago

The issue of running create.autoencoder() is due to the upgrade from Keras v2.x to Keras v3.5, the most current version.

Updating the R package keras to keras3 will resolve this issue. But to accommodate the update of keras3 will need a few following changes as well:

  1. Change the model output format from h5df to keras.
  2. Change the model loading function to load_model().
  3. Update the DESCRIPTION section and others.