An R wrapper for running the SigProfilerExtractor framework.
The purpose of this document is to provide a guide for using the SigProfilerExtractor framework to extract the De Novo mutational signatures from a set of samples and decompose the De Novo signatures into the COSMIC signatures. An extensive Wiki page detailing the usage of this tool can be found at https://osf.io/t6j7u/wiki/home/.
For users that prefer working in a Python environment, the tool is written in Python and can be found and installed from: https://github.com/AlexandrovLab/SigProfilerExtractor
*Reticulate has a known bug of preventing python print statements from flushing to standard out. As a result, some of the typical progress messages are delayed.
QUICK START GUIDE
This section will guide you through the minimum steps required to extract mutational signatures from genomes:
- First, install the python package using pip. The R wrapper still requires the python package:
pip install sigproextractor
- Open an R session and ensure that your R interpreter recognizes the path to your python installation:
$ R >> library("reticulate") >> use_python("path_to_your_python") >> py_config() python: /anaconda3/bin/python libpython: /anaconda3/lib/libpython3.6m.dylib pythonhome: /anaconda3:/anaconda3 version: 3.6.5 |Anaconda, Inc.| (default, Apr 26 2018, 08:42:37) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] numpy: /anaconda3/lib/python3.6/site-packages/numpy numpy_version: 1.16.1
If you do not see your python path listed, restart your R session and rerun the above commands in order.
- Install SigProfilerExtractorR using devtools:
- Load the package in the same R session and install your desired reference genome as follows (available reference genomes are: GRCh37, GRCh38, mm9, and mm10):
>> library("SigProfilerExtractorR") >> install("GRCh37", rsync=FALSE, bash=TRUE)
This will install the human 37 assembly as a reference genome.
Information about supported will be found at https://github.com/AlexandrovLab/SigProfilerMatrixGeneratorR
Signatures can be extracted from vcf files or tab delimited mutational table using the sigprofilerextractor function.
This will show the details about the sigprofilerextractor funtion.
>> library("SigProfilerExtractorR") >> path_to_example_data <- importdata("table") >> data <- path_to_example_data # here you can provide the path of your own data >> sigprofilerextractor("table", "example_output", data, minsigs=1, maxsigs=3, replicates=10, cpu=-1)
The example file will generated in the working directory
Decomposition of signatures to COSMIC signatures
SigProfilerExtractorR offer a separate function, decomposition, that decomposes a tab delimited file containing a set of De Novo signatures to the COSMIC signatures and attribute them to a given set of sample.
This will show the details about the decomposition function.
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.
Please address any queries or bug reports to S M Ashiqul Islam (Mishu) at m0islam.ucsd.edu