Here we have all the code related to the analysis presented in the "Functional impact of multi-omic interactions in breast cancer subtypes" by Soledad Ochoa and Enrique Hernández-Lemus Check https://github.com/mSolEdadO/TCGAmiRmethyRNAIntegration/tree/master/sgcca for history

Order to repeat the analysis

1. Get the data into matrixes
   1.1 getData.R
   1.2 prepro-mRNA.R
   1.3 prepro-miRNA.R
   1.4 prepro-methy.R,
   1.5 concatena.R
   1.6 mfa_normi.R
2. SGCCA
   2.1 fit_penalty.R
   2.2 choose_penalty.R
   2.3 sgcca.R
   2.4 sgccaSubsample.R
   2.5 joinSubsamples.R
3. SGCCA functional enrichment
   3.1 selectedFeatures.R
   3.2 functions_overrepre.R
   3.3 functions_overrepre_plots.R
   3.4 functions_overrepre_groups.R
   3.5 functionsJaccard.R
4. MI networks for the enriched functions
   4.1 get_matrix.R
   4.2 https://github.com/CSB-IG/ARACNE-multicore
   change run.sh because filenames are different
   line 12 → nom=$(echo $ftsv | cut -d'.' -f 1,2,3)
   line 23 → n=$( (cd adj; ls) | head -1 | cut -d'.' -f 4 )###check when MI is restricted
   4.3 MIfilter.R
   4.4 plotGraph.R
   4.5 annotateGraph.R