TDA-cancerSubtypes

R Code for

"A topological approach for cancer subtyping from gene expression data".

Reference:

Rafique, Omar, and A. H. Mir. "A topological approach for cancer subtyping from gene expression data." Journal of Biomedical Informatics 102 (2020): 103357.

To run the code, download and place all the files in one folder and open 'Subtyping_Lung_data.R'. Run this file line by line to replicate the results of the paper.

"Subtyping_Lung_data.R" contains the dimensionality reduction and topological clustering as explained in the paper. Some validation methods in the paper have been adapted from other works, especially https://github.com/angy89/RobustSparseCorrelation. Their code is available on this link but has been uploaded here too.