Gene Set Analysis Matlab (GSAM)

Gene set analysis (GSA) and visualization of results. This package was inspired by (and based on) the Piano package for R.

User guide

See the user guide for some examples on using GSAM.

Package contents

Run a gene set analysis (GSA)

• geneSetAnalysis - Run GSA

Gene set collection (GSC) import/export

• importGSC - Import gene set collection (GSC) from a .gmt file.
• exportGSC - Export a GSC to a .gmt or .txt file.
• extractMetaboliteGSC - Extract metabolite gene sets from a genome-scale model.
• extractSubsystemGSC - Extract subsystem gene sets from a genome-scale model.
• updateHumanGMTs - Generate several .gmt files from Human-GEM model.

Visualization of results

• GSAheatmap - Produce heatmap of single or multiple GSA results.
• genHeatMap - Generic heatmap function (used by GSAheatmap).
• genHeatScatter - Generic heatscatter function.

Additional functions

• adjust_pvalues - Adjust p-values for false discovery rate (FDR) (used by geneSetAnalysis).
• custom_cmap - Create or load a custom colormap (used by heatmap functions).
• modifyOptSettings - Helper function for assigning optional parameters.

Citation

Manuscript in preparation.