Question about getting WM and Wm

[Urrutia, Eugene]

Hi Lorraine,
Thank you for your interest in Canopy and the MARATHON pipeline.

please see our function MARATHON::falcon.output(). Usage within the pipeline is found in section 4.3.2 of the MARATHON notebook:
https://rawgit.com/yuchaojiang/MARATHON/master/notebook/MARATHON.html

In summary:

MARATHON::falcon.output() takes as input:
  readMatrix from variant data (section 4.3.1)
  tauhat from falcon::getChangepoints() followed by MARATHON::falcon.qc()
  cn from falcon::getASCN() followed by MARATHON::falcon.qc()
  
Then Canopy::canopy.sample() will require from the output
  Wm = Minor_copy
  WM = Major_copy
  Minor.sd = epsilonm
  Major_copy = epsilonM

Thanks, and please let us know if you have any other questions,
Gene

Begin forwarded message:

From: Lorraine Soudade <lsou...@gmail.com>
Subject: Message privé sur le sujet suivant : [canopy_phylogeny] Question about getting WM and Wm
Date: April 4, 2018 at 11:11:20 AM EDT
To: yj...@cornell.edu

Hello Yuchao,

A certain time ago you mentioned that you would automate the the WM & Wm generation with Falcon output. Do you have any R function or piece of code we could re-use to generate functional matrices from Falcon raw output files and directly give it as input for Canopy ?

Thank you,


Le lundi 7 novembre 2016 17:10:58 UTC+1, Yuchao Jiang a écrit :

    Hi Hai,

    Thanks for your interest in Canopy! Currently we have manual to generate WM and Wm using Sequenza (see under common questions https://github.com/yuchaojiang/Canopy ). We are working on automating the pipeline to generate this two matrices using Falcon and Falcon-X.

    Thanks and please feel free to let me know if you have any further questions.
    Yuchao

    --
    Yuchao Jiang (yuc...@mail.med.upenn.edu)
    PhD student in Genomics and Computational Biology
    University of Pennsylvania

    On Mon, Nov 7, 2016 at 7:11 AM, <bigh...@gmail.com> wrote:

        Hello Yuchao, I am confused about getting the WM and Wm.
        In your paper you used the FALCON's outputs.
        My first puzzle is that do you use the output from "getascn" function?
        And second puzzle is how to get read counts in the matched normal samples M(i,0) and m(i,0)?
        Did you just set the readMatrix in falcon the AT columns equal the AN columns so that M(i,0) and m(i,0) all equal 1?
        Thank you so much.