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.
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Update gene set annotations: Keep only genes present in the gene expression background. (
mean_pcor2_barcode_hallmark_estimates00.R) -
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,mean_pcor2_barcode_hallmark_estimates01.sh) -
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,mean_pcor2_barcode_hallmark_estimates02.sh) -
Aggregate results into a single data frame (
mean_pcor2_barcode_hallmark_estimates03.R)