Only interchromosomal SVs used for chr_breakpoint_enrichment and pval_exp_chr ?

[e-sollier]

Hello,

I want to use ShatterSeek, and I tried testing it on a sample which seems (based on visual inspection) to have a chromothripsis event on chromosome 3. In the chromSummary that I get, most fields seem coherent to me, but for some reason I get NA for the fields chr_breakpoint_enrichment and pval_exp_chr for chr3, even though there are 11 intrachromosomal SVs on this chromosome.

I had a quick look at the code to try to understand what cause the issue, and it looks like only interchromosomal SVs are considered for these tests (https://github.com/parklab/ShatterSeek/blob/master/R/function_criteria.R#L264), even though, based on my understanding of the ’chromosomal breakpoint enrichment test’ and ’random distribution of breakpoints test’, intrachromosomal SVs should be taken into account for these tests.

Is this the intended behavior, or am I misunderstanding something ?