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
- 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 - SGCCA
2.1 fit_penalty.R
2.2 choose_penalty.R
2.3 sgcca.R
2.4 sgccaSubsample.R
2.5 joinSubsamples.R - 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 - 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