Re: Code for simulation experiment in Canopy paper

[Jiang, Yuchao]

Hi,

Thanks for your interest. This work was published in 2016 and the simulation was performed a year or two before that. Attached are two scripts that I found. The simulation shouldn't be too hard -- if you assume the same tree topologies and use the same inputs as Canopy, you just need to generate your own Z, P, CM, Cm matrices as ground truths. From there, sample your R, X, WM, and Wm as input for Canopy. However, most of the other programs need different inputs — for example, the version of PhyloWGS that I used needs integer-valued copy number inputs which presumably have been adjusted for ploidy and purity.

Yuchao

On Mar 16, 2020, at 11:57 AM, ga...@mskcc.org wrote:

Dear Dr. Jiang,

My name is Teng and I am a researcher in the Papaemmanuil lab at MSKCC. We are interested in evaluating Canopy on our clinical sequencing data and were wondering if the source code is available for the simulation study presented in the 2016 paper. Thanks in advance!

Best,

Teng

Teng Gao

Computational Biologist

Sloan Kettering Institute

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