Re: Problems with Canopy

[Jiang, Yuchao]

Hi Quaid and Linda,

Most likely the wrong canopy sampling function was used. If there is no CNA, canopy.sample.nocna should be used. More info here https://github.com/yuchaojiang/Canopy/blob/master/instruction/sampling_mode.md

Yuchao

On Jan 27, 2018, at 12:16 PM, Quaid Morris <quaid....@gmail.com> wrote:

Thanks Nancy!

I have cc’ed Linda who found the issue.

Best,

Quaid

On Sat, Jan 27, 2018 at 11:52 AM Zhang, Nancy R <n...@wharton.upenn.edu> wrote:

Dear Quaid,

Sorry, I meant to reply earlier on this. The bug you found seems to be quite a simple issue, maybe an initialization condition or something. I am not familiar with the code, Yuchao is the author and he is on paternity leave ( his baby was just born two weeks ago!)  But given your reproducible example I don’t think this should be hard to fix once he gets back.  Thanks for your interest in our method!

Hope all is well!

Nancy

Sent from my iPhone

On Jan 18, 2018, at 7:45 AM, Quaid Morris <quaid....@gmail.com> wrote:

Hi folks,

Sorry for contacting you directly, one of the students that I am working with sent me an error report with some problems she encountered with Canopy. I didn't know where else to send the report

Best,

Quaid Morris, PhD
Associate Professor, The Donnelly Centre
Departments of Molecular Genetics and Computer Science
160 College St,  Rm 616
Toronto ON, M5S 3E1 Canada
http://morrislab.ca
cell:  (416) 220 5796

---------- Forwarded message ----------
From: Linda Sundermann <lsund...@uni-bielefeld.de>
Date: Wed, Jan 17, 2018 at 5:00 AM
Subject: Problems with Canopy
To: Quaid Morris <quaid....@gmail.com>

Hi Quaid,

as previously discussed, here is a detailed description of the error I get with Canopy, together with a minimal example.

The problem seems to be that Canopy is not working properly when no CNAs are present. The error message is the following:

Sample in tree space with 3 subclones
    Running chain 1 out of 2 ... 
Error in `colnames<-`(`*tmp*`, value = c("sna", "sna.st.node", "sna.ed.node" :
    length of 'dimnames' [2] not equal to array extent   
Calls: canopy.sample -> initialsna -> colnames<-  
Execution halted

I created a minimal example to reproduce this error and attached all files. Contained are all 7 files that Canopy needs as input. Described is only one SNA that appears is a segment with no CNAs. I also attached my scripts to start Canopy. These include
    - "input_example" that says where all files can be found and gives parameters
    - "start_canopy_script.sh" that starts Canopy with the given parameters
    - "execute_canopy.r" that contains the actual Canopy commands
Everything can be started by typing "cat input_example | ./start_canopy_script.sh".
All files need to be in the same folder.

I'd like to know whether it's possible to call Canopy with the given minimal example, so with only SNAs as input and no CNAs.

Thank you for your help,
cheers,
Linda

-- 
M.Sc. Linda Sundermann

Genome Informatics
Bielefeld University
Room: U10-141
Phone: +49 521 106 3840

---

WARNING: This e-mail has been altered by MIMEDefang.  Following this
paragraph are indications of the actual changes made.  For more
information about your site's MIMEDefang policy, contact
Wharton Email Services <postm...@wharton.upenn.edu>.  For more information about MIMEDefang, see:

            http://www.roaringpenguin.com/mimedefang/enduser.php3

An attachment named start_canopy_script.sh was removed from this document as it
constituted a security hazard.  If you require this document, please contact
the sender and arrange an alternate means of receiving it.

<execute_canopy.r>

<20180112_tmp_only_normal_epsilon_major.csv>

<20180112_tmp_only_normal_epsilon_minor.csv>

<20180112_tmp_only_normal_r.csv>

<20180112_tmp_only_normal_wmajor.csv>

<20180112_tmp_only_normal_wminor.csv>

<20180112_tmp_only_normal_x.csv>

<20180112_tmp_only_normal_y.csv>

<input_example>

--

Quaid Morris, PhD
Associate Professor, The Donnelly Centre
Departments of Molecular Genetics and Computer Science
160 College St,  Rm 616
Toronto ON, M5S 3E1 Canada
http://morrislab.ca
cell:  (416) 220 5796

[Linda Sundermann]

Thank you, Yuchao!

I will try this.

Best regards,
Linda

Am 1/28/18 um 8:07 AM schrieb Jiang, Yuchao: