Does the following seem like a good method to assign a p-value for segment DUPLICATION or DELETION, to each segment in the dnacopy.seg file?
1. Use PureCN's readCurationFile to read the .rds file into object RDS, then retrieve the log ratios of the marks in RDS$input$log.ratio
2. Compute the adjusted copy ratio of each mark by taking 2^log.ratio, then applying the purity/ploidy adjustment equation to the result, using purity and ploidy from the curation file.
3. Use a Wilcoxon 1-sample test to test whether the resulting copy ratios are significantly greater, or less, than 1.