CNV visualization

[ramonv...@gmail.com]

Hello Yuchao,

After I successfully generate the CNVs file, I'm having some trouble with IGV visualization code! 

First of all, i'm getting some problems to understand the tumorname_lookup.txt (even thought after reading your comments on: https://groups.google.com/forum/#!msg/codex2/5EEaFc4Ld9Y/PJAtRFR-BQAJ). This file is an only sample names file or do i have to have other information in this file? With an only sample names file i'm getting this Error in the further steps:

Error in tumorsampname[i, 3] : subscript out of bounds

Calls: paste

Execution halted

I tried to resolve this setting tumorsampname[i,1], this made the script keep running until it hits another Error:

Error in file(file, ifelse(append, "a", "w")) : 

  cannot open the connection

Calls: write.table -> file

In addition: Warning message:

In file(file, ifelse(append, "a", "w")) :

  cannot open file 'codex_segments/101.sor.codex.codex.seg.txt': No such file or directory

Do you have any suggestions on how do I resolve this?

Other question I would like to ask you is about other methods of visualization, it's possible to use cnv.plot of cnv.kit 1.66 to plot the cnvs? If so, where do I extract the BATCH information?

Do you recommend any other methods for visualization?

I'm struggling to do nice plots with the final call segmentation file that I generated.

Thanks for your help,

Ramon