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MutSpec-Compare

Computes the similarity between the signatures identified by MutSpec-NMF and a set of published signatures using the cosine similarity method.

Input format

  • A matrix containing the signatures identified by MutSpec-NMF.
    The input matrix can be found in MutSpec-NMF ouput folder: NMF/Files/MatrixW-Normto100.txt

  • A matrix containing a set of published signatures.

Two set of published signatures are provided:

  • Frequency-COSMIC30-Hupki.txt: Contains the 30 mutational signatures operative in human cancer from COSMIC and 4 experimental signatures obtained in mouse cells for AA, MNNG, BaP and AID published by Olivier et al.
  • Frequency-COSMIC30-Hupki-Others.txt: Contains in addition experimental signatures obtained in mouse model for DMBA published by Nassar et al., MNU and Urethane published by Westcott et al..

Output

Heatmap showing the cosine similarity between the signatures identified by MutSpec-NMF and a set of published signatures.

Usage

Rscript R/compareSignature_Galaxy.r Frequency-COSMICv72-Hupki.txt outfolder_MutSpec-NMF/NMF/Files/MatrixW-Inputggplot2.txt output_dir_MutSpec-NMF/NMF/

List of parameters:

Parameter Description
Published_Signature Matrix containing a set of published signatures
New_Signature Matrix containing the signatures identified by MutSpec-NMF
Output_Folder Output directory