Suggested_Solution Directory

This section explains each of the files and folders in the Suggested_Solution directory in detail. Many of the files are similar to the files found in Output - All Solutions and it is recommended to refer to that section for similar files. The files that are original to this directory will be indicated.

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Output Overview

Here is an overview of the file structure for Suggested_Solution:

In the following sections, the files that differ from those found All_Solutions will be examined.

COSMIC_SBS96_Decomposed_Solution

There are two files in COSMIC_SBS96_Decomposed_Solution that are not found in All_Signatures.

1. De_Novo_map_to_COSMIC_SBS96.csv
2. SBS96_Decomposition_Plots.pdf

De_Novo_map_to_COSMIC_SBS96.csv

This file contains data on the de novo extracted signatures and the COSMIC signatures that compose them. Additionally information on the L1 error %, L2 error %, KL divergence, cosine similarity, and correlation.

Below is an example of what the file contains.

SBS96_Decomposition_Plots.pdf

This file contains a visualization of the results from De_Novo_map_to_COSMIC_SBS96.csv. There are two plots to the left of the curly brace. One is the original de novo signature plot and the other is the reconstruction of the de novo signature. On the right side of the curly brace are the COSMIC signatures that the de novo signature is composed of. Additionally, below the reconstructed plot are the data for cosine similarity, correlation, L1 error %, L2 error %, and KL divergence.

De_Novo_Solution

There are two files in the De_Novo_Solution directory not found in All_Signatures.

1. De_Novo_Mutation_Probabilities_refit.txt
2. SBS96_De-Novo_refit_Signature_Assignment_log.txt

De_Novo_Mutation_Probabilities_refit.txt

This file contains the mutation probability for each sample and identified signature. Each of the signature mutation probabilities for a sample add up to 1.

Below is an example of the first few lines of the example file.

SBS96_De-Novo_refit_Signature_Assignment_log.txt

This file logs the events that occur when COSMIC signatures are assigned to samples.

Below is an example of the start of the log file.