Extracts mutational signatures from mutational catalogues

# SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting. Detailed documentation can be found at: https://osf.io/t6j7u/wiki/home/

## Installation

To install the current version of this Github repo, git clone this repo or download the zip file. Unzip the contents of SigProfilerExtractor-master.zip or the zip file of a corresponding branch.

In the command line, please run the following:

$cd SigProfilerExtractor-master$ pip install .


For most recent stable pypi version of this tool, In the command line, please run the following:

$pip install SigProfilerExtractor  Install your desired reference genome from the command line/terminal as follows (available reference genomes are: GRCh37, GRCh38, mm9, and mm10): $ python
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install('GRCh37')


This will install the human 37 assembly as a reference genome. You may install as many genomes as you wish.

Next, open a python interpreter and import the SigProfilerExtractor module. Please see the examples of the functions.

## Functions

The list of available functions are:

• importdata
• sigProfilerExtractor
• estimate_solution
• decompose

• plotActivity.py

### importdata

Imports the path of example data.

importdata(datatype="matrix")


#### importdata Example

from SigProfilerExtractor import sigpro as sig
path_to_example_table = sig.importdata("matrix")
data = path_to_example_table
# This "data" variable can be used as a parameter of the "project" argument of the sigProfilerExtractor function.

# To get help on the parameters and outputs of the "importdata" function, please use the following:
help(sig.importdata)


### sigProfilerExtractor

Extracts mutational signatures from an array of samples.

sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37", opportunity_genome = "GRCh37", context_type = "default", exome = False,
minimum_signatures=1, maximum_signatures=10, nmf_replicates=100, resample = True, batch_size=1, cpu=-1, gpu=False,
nmf_init="random", precision= "single", matrix_normalization= "gmm", seeds= "random",
min_nmf_iterations= 10000, max_nmf_iterations=1000000, nmf_test_conv= 10000, nmf_tolerance= 1e-15, get_all_signature_matrices= False)

Category Parameter Variable Type Parameter Description
Input Data
input_type String The type of input:
output String The name of the output folder. The output folder will be generated in the current working directory.
input_data String
Path to input folder for input_type:
• vcf
• bedpe
Path to file for input_type:
• matrix
• seg:TYPE
reference_genome String The name of the reference genome. The default reference genome is "GRCh37". This parameter is applicable only if the input_type is "vcf".
opportunity_genome String The build or version of the reference genome for the reference signatures. The default opportunity genome is GRCh37. If the input_type is "vcf", the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (GRCh37, GRCh38, mm9, mm10 and rn6). If a different opportunity genome is selected, the default genome GRCh37 will be used.
context_type String A string of mutaion context name/names separated by comma (","). The items in the list defines the mutational contexts to be considered to extract the signatures. The default value is "96,DINUC,ID", where "96" is the SBS96 context, "DINUC" is the DINUCLEOTIDE context and ID is INDEL context.
exome Boolean Defines if the exomes will be extracted. The default value is "False".
NMF Replicates
minimum_signatures Positive Integer The minimum number of signatures to be extracted. The default value is 1.
maximum_signatures Positive Integer The maximum number of signatures to be extracted. The default value is 25.
nmf_replicates Positive Integer The number of iteration to be performed to extract each number signature. The default value is 100.
resample Boolean Default is True. If True, add poisson noise to samples by resampling.
seeds String It can be used to get reproducible resamples for the NMF replicates. A path of a tab separated .txt file containing the replicated id and preset seeds in a two columns dataframe can be passed through this parameter. The Seeds.txt file in the results folder from a previous analysis can be used for the seeds parameter in a new analysis. The Default value for this parameter is "random". When "random", the seeds for resampling will be random for different analysis.
NMF Engines
matrix_normalization String Method of normalizing the genome matrix before it is analyzed by NMF. Default is value is "gmm". Other options are, "log2", "custom" or "none".
nmf_init String The initialization algorithm for W and H matrix of NMF. Options are 'random', 'nndsvd', 'nndsvda', 'nndsvdar' and 'nndsvd_min'. Default is 'random'.
precision String Values should be single or double. Default is single.
min_nmf_iterations Integer Value defines the minimum number of iterations to be completed before NMF converges. Default is 10000.
max_nmf_iterations Integer Value defines the maximum number of iterations to be completed before NMF converges. Default is 1000000.
nmf_test_conv Integer Value defines the number number of iterations to done between checking next convergence. Default is 10000.
nmf_tolerance Float Value defines the tolerance to achieve to converge. Default is 1e-15.
Execution
cpu Integer The number of processors to be used to extract the signatures. The default value is -1 which will use all available processors.
gpu Boolean Defines if the GPU resource will used if available. Default is False. If True, the GPU resources will be used in the computation. Note: All available CPU processors are used by default, which may cause a memory error. This error can be resolved by reducing the number of CPU processes through the cpu parameter.
batch_size Integer Will be effective only if the GPU is used. Defines the number of NMF replicates to be performed by each CPU during the parallel processing. Default is 1.
Solution Estimation Thresholds
stability Float Default is 0.8. The cutoff thresh-hold of the average stability. Solutions with average stabilities below this thresh-hold will not be considered.
min_stability Float Default is 0.2. The cutoff thresh-hold of the minimum stability. Solutions with minimum stabilities below this thresh-hold will not be considered.
combined_stability Float Default is 1.0. The cutoff thresh-hold of the combined stability (sum of average and minimum stability). Solutions with combined stabilities below this thresh-hold will not be considered.
allow_stability_drop Boolean Default is False. Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered.
Decomposition
cosmic_version Float Takes a positive float among 1, 2, 3, 3.1, 3.2 and 3.3. Default is 3.3. Defines the version of the COSMIC reference signatures.
make_decomposition_plots Boolean Defualt is True. If True, Denovo to Cosmic sigantures decompostion plots will be created as a part the results.
collapse_to_SBS96 Boolean Defualt is True. If True, SBS288 and SBS1536 Denovo signatures will be mapped to SBS96 reference signatures. If False, those will be mapped to reference signatures of the same context.
Others
get_all_signature_matrices Boolean If True, the Ws and Hs from all the NMF iterations are generated in the output.
export_probabilities Boolean Defualt is True. If False, then doesn't create the probability matrix.

#### sigProfilerExtractor Example

VCF Files as Input

from SigProfilerExtractor import sigpro as sig
def main_function():
# to get input from vcf files
path_to_example_folder_containing_vcf_files = sig.importdata("vcf")
# you can put the path to your folder containing the vcf samples
data = path_to_example_folder_containing_vcf_files
sig.sigProfilerExtractor("vcf", "example_output", data, minimum_signatures=1, maximum_signatures=3)
if __name__=="__main__":
main_function()
# Wait until the excecution is finished. The process may a couple of hours based on the size of the data.
# Check the current working directory for the "example_output" folder.


Matrix File as Input

from SigProfilerExtractor import sigpro as sig
def main_function():
# to get input from table format (mutation catalog matrix)
path_to_example_table = sig.importdata("matrix")
data = path_to_example_table # you can put the path to your tab delimited file containing the mutational catalog matrix/table
sig.sigProfilerExtractor("matrix", "example_output", data, opportunity_genome="GRCh38", minimum_signatures=1, maximum_signatures=3)
if __name__=="__main__":
main_function()


### Estimation of the Optimum Solution

Estimate the optimum solution (rank) among different number of solutions (ranks).

estimate_solution(base_csvfile="All_solutions_stat.csv",
All_solution="All_Solutions",
genomes="Samples.txt",
output="results",
title="Selection_Plot",
stability=0.8,
min_stability=0.2,
combined_stability=1.0,
allow_stability_drop=False,
exome=False)

Parameter Variable Type Parameter Description
base_csvfile String Default is "All_solutions_stat.csv". Path to a csv file that contains the statistics of all solutions.
All_solution String Default is "All_Solutions". Path to a folder that contains the results of all solutions.
genomes String Default is Samples.txt. Path to a tab delimilted file that contains the mutation counts for all genomes given to different mutation types.
output String Default is "results". Path to the output folder.
title String Default is "Selection_Plot". This sets the title of the selection_plot.pdf
stability Float Default is 0.8. The cutoff thresh-hold of the average stability. Solutions with average stabilities below this thresh-hold will not be considered.
min_stability Float Default is 0.2. The cutoff thresh-hold of the minimum stability. Solutions with minimum stabilities below this thresh-hold will not be considered.
combined_stability Float Default is 1.0. The cutoff thresh-hold of the combined stability (sum of average and minimum stability). Solutions with combined stabilities below this thresh-hold will not be considered.
allow_stability_drop Boolean Default is False. Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered.
exome Boolean Default is "False". Defines if exomes samples are used.

#### Estimation of the Optimum Solution Example

from SigProfilerExtractor import estimate_best_solution as ebs
ebs.estimate_solution(base_csvfile="All_solutions_stat.csv",
All_solution="All_Solutions",
genomes="Samples.txt",
output="results",
title="Selection_Plot",
stability=0.8,
min_stability=0.2,
combined_stability=1.0,
allow_stability_drop=False,
exome=False)


#### Estimation of the Optimum Solution Output

The files below will be generated in the output folder:

File Name Description
All_solutions_stat.csv A csv file that contains the statistics of all solutions.
selection_plot.pdf A plot that depict the Stability and Mean Sample Cosine Distance for different solutions.

### Decompose

For decomposition of denovo signatures please use SigProfilerAssignment

### Activity Stacked Bar Plot

Generates a stacked bar plot showing activities in individuals

plotActivity(activity_file, output_file = "Activity_in_samples.pdf", bin_size = 50, log = False)

Parameter Variable Type Parameter Description
activity_file String The standard output activity file showing the number of, or percentage of mutations attributed to each sample. The row names should be samples while the column names should be signatures.
output_file String The path and full name of the output pdf file, including ".pdf"
bin_size Integer Number of samples plotted per page, recommended: 50

#### Activity Stacked Bar Plot Example

\$ python plotActivity.py 50 sig_attribution_sample.txt test_out.pdf


## Video Tutorials

Take a look at our video tutorials for step-by-step instructions on how to install and run SigProfilerExtractor on Amazon Web Services.

### GPU support

If CUDA out of memory exceptions occur, it will be necessary to reduce the number of CPU processes used (the cpu parameter).

## Citation

Islam SMA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, and Alexandrov LB (2022) Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. Cell Genomics. doi: 10.1016/j.xgen.2022.100179.

This software and its documentation are copyright 2018 as a part of the sigProfiler project. The SigProfilerExtractor framework is free software and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

## Contact Information

Please address any queries or bug reports to Mark Barnes at mdbarnes@ucsd.edu

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