I updated to a newer version of PureCN and ran into a problem in my post-processing of PureCN output from callLOH. The problem was caused by NA values in the "M" column. My previous PureCN version never had NA values in the column. The PureCN doc file doesn't mention NA in its description of the "M" column. Is there a problem, or is NA expected and just means PureCN is unable to estimate M?

I'd like to suggest whenever possible, the doc files should be updated to indicate changes such as this, and furthermore, since they may have an effect on the user's downstream processing, they should be mentioned in the release notes. Thanks.

Yes, the callLOH function changed and I actually mention this in the NEWS file ( http://bioconductor.org/packages/release/bioc/news/PureCN/NEWS ).

LOH calling requires heterozygous SNPs, so NA means no SNPs. The change of defaults was necessary because some users were not aware that segments without SNPs were missing from this output.