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Advanced Mode Examples

This section provides examples for advanced users to get started with using SigProfilerAssignment for de novo extraction of mutational signautres downstream analysis, including:

  1. Assignment of de novo extracted mutational signatures using denovo_fit.
  2. Decomposition of de novo extracted mutational signatures using a known set of signatures (reference [COSMIC][4] signatures or customized signature databases) by decompose_fit.

denovo_fit

Attributes the somatic mutations of a given sample/s to a set of input de novo signatures.

Two input files are required. First, a file containing the input somatic mutations, in any of the formats specified in the Using the Tool - Input section. Also, a matrix containing the de novo extracted mutational signatures, commonly derived from SigProfilerExtractor.

Note: A reference genome build should also be specified if a mutation calling file is used as input.

$ python
>> from SigProfilerAssignment import Analyzer as Analyze
>> Analyze.denovo_fit(samples="path/to/input/mutations/file",
                   output="path/to/output/folder",
                   input_type="desired/input/mutation/file/format",
                   signatures="path/to/input/denovo/signatures/file",
                   genome_build="GRCh37")

You can also run SigProfilerAssignment denovo_fit function from command line: 

$ SigProfilerAssignment denovo_fit "path/to/input/mutations/file" "path/to/output/folder" --input_type "desired/input/mutation/file/format" --signatures "path/to/input/denovo/signatures/file" --genome_build "GRCh37"

decompose_fit

Decomposes a set of de novo extracted mutational signatures into a known set of signatures (reference COSMIC signatures or customized signature databases) and assigns these known signatures into a given sample/s.

Two input files are required. First, a file containing the input somatic mutations, in any of the formats specified in the Using the Tool - Input section. Also, a matrix containing the de novo extracted mutational signatures, commonly derived from SigProfilerExtractor.

An optional third input file is needed in case a custom reference signature database is used. By default, reference COSMIC signatures v3.5 are used for decomposing the set of de novo extracted signatures.

Note: A reference genome build should also be specified if a mutation calling file is used as input.

$ python
>> from SigProfilerAssignment import Analyzer as Analyze
>> Analyze.decompose_fit(samples="path/to/input/mutations/file", 
                      output="path/to/output/folder",
                      input_type="desired/input/mutation/file/format",
                      signatures="path/to/input/denovo/signatures/file",
                      signature_database="path/to/optional/reference/signatures/database/file",
                      genome_build="GRCh37")

You can also run SigProfilerAssignment decompose_fit function from command line: 

$ SigProfilerAssignment decompose_fit "path/to/input/mutations/file" "path/to/output/folder" --input_type "desired/input/mutation/file/format" --signatures "path/to/input/denovo/signatures/file" --signature_database "path/to/optional/reference/signatures/database/file" --genome_build "GRCh37"