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Decomposes mutational catalogues to mutational signatures

Project description

SigProfilerSingleSample

SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator, SigProfilerExtractor and SigProfilerPlotting.

INSTALLATION

In the commandline, please type the following line:

$pip install sigproSS

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.

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

FUNCTIONS

importdata

Imports the path of example data.

importdata()

Example: 
-------
>>> from sigproSS import spss 
>>> data = spss.importdata()
This "data" variable can be used as a parameter of the first argument of the sigproSS function.

To get help on the parameters and outputs of the "importdata" function, please write down the following line:

>>> help(spss.importdata)

single_sample

Decompose the query samples into the global signatures.

single_sample(vcf, outputdir, exome=False)

Example: 
-------
>>> from sigproSS import spss 
>>> data = spss.importdata()
>>> spss.single_sample(data, "results", ref="GRCh37", exome=False)

To get help on the parameters and outputs of the "importdata" function, please write down the following line:

>>> help(spss.single_sample)

COPYRIGHT

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 S M Ashiqul Islam (Mishu) at m0islam.ucsd.edu

Project details


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