DECoN v2.0.1 installation error, Rscript error and question. about decon

[tomdrake]

Hello

Just to add to this issue so others know!

Installing this package does not work according to the instructions and the code is full of errors as outlined above. I installed as per instructions into the correct version of R, >4.2.0, but there have been underlying changes to other packages. For example ExomeDepth will add a GC column when a FASTA is specified, but DECoN will then erroneously label this as a sample count column (So make sure to use the 1.15 release of ExomeDepth if you get this working or edit the code to avoid the FASTA argument...).

Using the packrat version of DECoN may be a better work around.

As DECoN appears to be a wrapper for ExomeDepth, I have had far more success with ExomeDepth for calling CNVs and getting them in the right shape. The package is well maintained and has good vignettes for how to analyse specific chromosomal CNVs. It works without having to rewrite or edit code.

https://cran.r-project.org/web/packages/ExomeDepth/index.html

For X chromosome copy number, that's more tricky! Would split by sex to begin, or you could even sum/ merge your counts in your BAM file and treat it as one (so if you have overall any amplification/deletion).

Hope this helps

Tom

[emunte]

Hello,

Thanks for your comments, I think they are very useful.
I just want to add a suggestion:
Instead of replacing colnames(ExomeCount)[1:length(sample.names)+4]=sample.names for colnames(ExomeCount)[1:length(sample.names)+5]=sample.names

I would put the following:

if(names(ExomeCount)[5]=="GC"){ colnames(ExomeCount)[1:length(sample.names)+5]=sample.names #assigns the sample names to each column }else{ colnames(ExomeCount)[1:length(sample.names)+4]=sample.names }

The thing is that if you leave the --fasta parameter NULL in ReadInBams.R then RData dataframe generated has 1 less column because GC content is not computed, so GC column does not exist.

Again thank you for your comments!

Best regards,

Eli

[mcollodetti]

Hi guys!

I am relieved to know that other had issues as well. Installing DECoN became a challenge. Is anyone considering recording a video on how to install it on Windows?