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PCxN Version Submitted to PLOS Computational Biology
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Version submitted to PLOS Computational Biology

The scripts to get the pathway correlation estimates are in the src folder. Below is a brief overview of the scripts.

  1. Update gene set annotations: Keep only genes present in the gene expression background. (mean_pcor2_barcode_hallmark_estimates00.R)

  2. Get experiment-level estimates: For each experiment, estimate all pairwise pathway correlation coefficients along with the corresponding p-values. (mean_pcor2_barcode_hallmark_estimates01.R,

  3. Combine experiment-level estimates: Aggregate the experiment-level correlation estimates using a weighted average, and the experiment-level p-values using Liptak's method. (mean_pcor2_barcode_hallmark_estimates02.R,

  4. Aggregate results into a single data frame (mean_pcor2_barcode_hallmark_estimates03.R)

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