Quick Start Example

This section provides a quick start guide for using SigProfilerMatrixGenerator.

Step 1: Start Python

Start a Python terminal session and verify you're running Python 3:

python3

You should see output like:

Python 3.5.2 (v3.5.2:4def2a2901a5, Jun 26 2016, 10:47:25)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

Step 2: Verify Installation

Check if SigProfilerMatrixGenerator is installed:

>>> help("modules")

Look for SigProfilerMatrixGenerator in the list of available modules.

If not installed, follow the instructions on the Installation - Python page.

Step 3: Install Reference Genome

Install your desired reference genome:

>>> from SigProfilerMatrixGenerator import install as genInstall
>>> genInstall.install('GRCh37')

This example installs the human GRCh37 assembly. You can install any of the available genome assemblies.

Note: - ~3 GB of storage is required per genome - This step may take some time due to large file sizes

Step 4: Prepare Input Files

Place your VCF files in your desired project folder. We recommend naming it based on your project's name.

Supported input formats: - VCF (Variant Call Format) - one file per sample - MAF (Mutation Annotation Format) - ICGC format - Simple text files (tab-delimited)

Step 5: Generate Matrices

From within a Python session, generate the matrices:

>>> from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen
>>> matrices = matGen.SigProfilerMatrixGeneratorFunc("test", "GRCh37", "/Users/user/Desktop/test", plot=True)

Parameter Layout

SigProfilerMatrixGeneratorFunc(project, reference_genome, path_to_input_files, plot)

Parameter	Description
`project`	Your project name (string)
`reference_genome`	Reference genome to use (e.g., "GRCh37", "GRCh38")
`path_to_input_files`	Full path to directory containing your input VCF files
`plot`	Set to `True` to generate visualization plots

Expected Output

After successful execution, you will find the following in your output directory:

project_name/
├── input/          # Copies of input files
├── logs/           # Log and error files
└── output/
    ├── SBS/        # Single base substitution matrices
    ├── DBS/        # Double base substitution matrices
    ├── ID/         # Insertion/deletion matrices
    ├── TSB/        # Transcriptional strand bias results
    ├── plots/      # Visualization plots (if plot=True)
    └── vcf_files/  # Processed VCF files

Complete Example

# Start Python
python3

# Import the module
>>> from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen

# Generate matrices with plotting enabled
>>> matrices = matGen.SigProfilerMatrixGeneratorFunc(
...     "my_cancer_project",      # project name
...     "GRCh37",                  # reference genome
...     "/path/to/my/vcf/files",  # input directory
...     plot=True                  # generate plots
... )

For all function arguments and their types, see the Using the Tool - SBS, ID, DBS Input section.