mutspec_nmf.md

MutSpec-NMF

Extract mutational signatures composed of 96 SBS types (6 SBS types in their trinucleotide sequence context) using the non-negative matrix (NMF) factorisation algorithm of Brunet with the Kullback-Leibler divergence penalty implemented in the R package NMF.

Input format

Input matrix created with the tool MutSpec-Stat.
The input matrix can be found in MutSpec-Stat ouput folder: Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt

Output

• Composition of mutational signatures and contribution of each signature to each sample.
• Input matrix for the tool MutSpec-Compare.

Usage

Rscript R/somaticSignature_Galaxy.r --input outfolder_MutSpec-Stat/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt --nbSignature 2 --cpu 8 --output output_dir

List of parameters:

Parameter	Description
--input	Input matrix created with the tool MutSpec-Stat
--nbSignature	Number of signatures to extract (min=2)
--cpu	Number of CPUs
--output	Output directory
--html	Path to HTML page (ONLY FOR GALAXY WRAPPER)
--help	Print help message