The molecular_time_customized from shaghayeghsoudi

molecular_time_customized's Introduction


IMPORTANT NOTE: The original "mol_time.R" script has been modified by Shaghayegh Soudi ("mol_time_cutomized.R") to adjust cases where the SNV clusteing (based on SNV allele frequency) does not match with the CNV segment status. I observed this problem can occur when the purity estimation is not good enough and some modifications have been included in the original package to avoid the package stop working in a module or pipeline. The changes have been annotated in mol_time_cutomized.R.
Modified by Shaghayegh Soudi (March 2021)

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R function for calculating the timing of DNA aberration events from 
NGS data.

Written by Peter Campbell and Francesco Maura (May 2017)
Tidy up/restructuring by Nicos  Angelopoulos, (2017/06/07)

This software is distributed under the MIT license:
https://opensource.org/licenses/MIT

To load simply do 
% R
> source("mol_time.R")

To run call the function with something like,
> mol_time(data.dir="data", res.dir="res-defaults")

To see if you getting the same results to ours, compare the 
outputs of the above call to the files in directory "test-defaults".

See documentation in man/mol_time.pdf

Authors: Peter Campbell, Francesco Maura & Nicos Angelopoulos
Maintainer & docs: Nicos Angelopoulos

CASM: Cancer Ageing and Somatic Mutations
Wellcome Sanger Institute, 
June, 2017 - Jan, 2018
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http://www.sanger.ac.uk/science/programmes/cancer-genetics-and-genomics

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