Visualization error

[andrisvAria]

Hi, I am trying to visualize cnv calls from example1 of PennCNV but I have two problems. First, when I run visualize_cnv.pl -format plot -signal offspring.txt ex1.rawcnv I get this output

NOTICE: Signal values for 4 CNV regions are found in offspring.txt NOTICE: Processing sample offspring.txt CNV chr11:55603545-55669650 with copy number of 0 ... written to offspring.txt.chr11.55603545.PDF NOTICE: Processing sample offspring.txt CNV chr11:81792950-81806219 with copy number of 1 ... Use of uninitialized value in numeric gt (>) at C:\Users\andsav\Desktop\PennCNV-1.0.5\PennCNV-1.0.5\visualize_cnv.pl line 204. written to offspring.txt.chr11.81792950.PDF NOTICE: Processing sample offspring.txt CNV chr20:10511631-10583260 with copy number of 1 ... written to offspring.txt.chr20.10511631.PDF NOTICE: Processing sample offspring.txt CNV chr3:3957986-4054960 with copy number of 1 ... written to offspring.txt.chr3.3957986.PDF

I wonder, what does this mean Use of uninitialized value in numeric gt (>) at C:\Users\andsav\Desktop\PennCNV-1.0.5\PennCNV-1.0.5\visualize_cnv.pl line 204. and how does it affect me?

Then, when I want to look at the generated plots, I was under the impresion that they will exist in jpg format in the folder. instead I have this

If I open one of them using Rstudio, it gives me the followin error Error in file(file, "rt") : cannot open the connection In addition: Warning messages: 1: file ‘.RData’ has magic number 'RDX3' Use of save versions prior to 2 is deprecated 2: In file(file, "rt") : cannot open file 'offspring.txt.chr11.81792950.signal': No such file or directory

Any ideas on what could be wrong and what I need to do to fix this?

System INFO I use windows 10 x64, installed ActivePerl 5.8 x32 and have R 3.6.0

[nitzzzzzzz]

Hi andrisvAria, Facing same issue. have you fixed it? if yes, how did you fix it? my system info is same as of you. thanks

[andrisvAria]

Hey @nitzzzzzzz . Unfortunately I can't find the exact solution since it was such a long time ago. But, I do remember it was an issue with this library [https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html].

[nitzzzzzzz]

I just used jpeg r function [https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html] instead of bitmap in cnv_visualize.pl like

jpeg(filename=""Rplot%03d.jpeg"",width=3,height=3,units="in",res=300,pointsize=6) and the issue is resolved.

Thank you andrisvAria for help ---------------------------------------- ---------------------------------------- With Regards

NITESH KUMAR SHARMA

PhD Research Scholar (Bioinformatics) Centre For Agricultural Bioinformatics ICAR-Indian Agricultural Statistics Research Institute Library Avenue, Pusa, New Delhi, 110012 Ph- (+91) 8506891991

On Wed, Jan 12, 2022 at 4:12 PM andrisvAria @.***> wrote:

Hey @nitzzzzzzz https://github.com/nitzzzzzzz . Unfortunately I can't find the exact solution since it was such a long time ago. But, I do remember it was an issue with this library [https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html].

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[kaichop]

Thank you for the help addressing the issue. I am not very familiar with R, so I cannot really tell why sometimes PDF is not generated; it is good to know that PNG/JPG can work instead.