plot_cnvs() fails due to gene_pattern variable in atlas_cnv.R

[c-roca]

Hi, I tried to run Atlas-CNV and I was getting and error that has not been reported yet in the atlas_cnv.R script, in the plot_cnvs() function.

The pipeline was working fine until it had to plot genes with more than 2 Exons, in my case the error happened with the gene DICER1. The error that I was getting indicated that " ^DICER1-" couldn't be found in ppp$Gene_Exon so the variable gene_exon_all was empty and the pipeline stopped running.

After checking line by line, I could fix it by commenting the following line (line 225 in atlas_cnv.R aprox):

gene_pattern = paste('^', cnv_genes_2plot[g], '-', sep='') # bug: grep 'NF2' gets 'RNF207'

and loading the variable gene_pattern with the unformatted gene name so the code could keep running:

gene_pattern=gene

which seems to be added to fix a previous bug.

After that, the pipeline worked fine and I could plot the CNVs correctly.

Could this be applied in a new version of the pipeline so the installation works?

Thanks in advance, C-roca