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README_integ.md

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Basic integrative analyses


source("/path/to/beataml_genomics/analyses/baml_lasso.R")

preprocess()

The result is an RData file preproc_data.RData containing the expected inputs.

An actual run can be carried out using run.combined.datatypes(), producing an RData file lasso_results.RData consisting of two objects:

  1. pred.sum: A data.table consisting of the predicted and test AUC values for each sample, inhibitor and repetition
  2. coef.list: A list with one element per drug containing a matrix of estimated coefficients (nrows) per bootstrap and repetition (columns).