Unable to run CNView.R

[GreeshmaThulasi]

Hi,
I created a .bed file for a single sample as,
Chr Start End sampleNA-78
chr1 10173 10230 1
chr1 10458 10603 1
chr1 11081 11227 1
chr1 11228 11256 1
chr1 11854 12022 1
chr1 12646 12780 1
chr1 12792 12837 1
chr1 12837 12858 2
chr1 12858 12914 3
chr1 12914 12915 2
chr1 12915 12955 3
chr1 12955 12963 2
chr1 12963 12964 1
chr1 12964 12984 2
chr1 12984 13034 1
chr1 13447 13512 3
chr1 13512 13592 4
chr1 13592 13661 1
chr1 13794 13917 1
when I executed CNView.R as,
Rscript /home/ngslab/Downloads/CNView-master/CNView.R 21 35919400 36903600 sampleNA-78 /home/ngslab/src/samtools/bam_files/new.bed sampleAexampleplot.pdf --title "exampleplot"
But, I'm getting the following error,
Loading required package: optparse
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘optparse’
Error in make_option(c("-c", "--compression"), type = "integer", default = NULL, :
could not find function "make_option"
Execution halted
Please help me to resolve the problem.

[RCollins13]

Hi @GreeshmaThulasi,

Thanks for your interest in CNView.

The error is because the optparse library is not installed. If you need help solving this problem, I'd recommend starting here.

Aside from the error, there are a few issues with this use case that are worth mentioning:

• CNView doesn't work for datasets of individual samples. It requires a at least one other (and ideally >30 other) samples that do not carry the CNV of interest to normalize sequencing coverage in that region. Please add >30 additional samples to your input coverage matrix, if you have them.

• The bins specified in your example BED file are neither sequential nor uniformly sized, both of which are requirements for CNView. Please review the CNView Getting Started Documentation for examples and more specifications. Please make sure your input BED file matches the format of the example provided in the CNView documentation.

• The coverage of this sample looks very low. I would not expect CNView to work well on such low-coverage libraries. CNView was designed for samples with medium-to-high coverage whole-genome sequencing. You can get around this by using larger bin sizes (e.g. 1kb or 10kb sequential bins), but of course this will limit the resolution for visualizing CNVs.

Hope this helps,
Ryan