kiranjavkar / cmsc828p_project1

Project 1a: Mutation Signatures

For this project, you will implement and run the NMF mutation signature decomposition described in Alexandrov, et al. (Cell Reports, 2013) on the data from Alexandrov, et al. (Nature, 2013).

Data

The input data for your algorithm is a mutation count matrix. The mutation count matrices are stored in a tab-separated text file, where each line lists the number of mutations of a given category for a single patient. The patient name will be stored in the first column, and the category names in the first row.

Example data

You can find a small example dataset for your project in data/examples. The examples directory also includes the signatures used to generate the data, which you can use to sanity check your results.

Real data

You will need to download real data for your project and process it into the same format as the example data. You can find the Pan-Cancer mutation counts originally used by Alexandrov, et al. (Nature, 2013) at ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl.