hello,
i'm currently working on a proteogenomics project, and i am using customProDB to generate a custom DB, it's a great R package and i find it really helpful.
During the process and while trying to generate my novel junctions peptides fasta, I believe that I ran into a little bug.
at line 131 in the function JunctionType.R "if(length(index_NA) >= 0) matchid_new <- matchid[-index_NA, ]" the if condition will have a true value either if (length(index_NA) is equal to or greater than 0, in the case when (length(index_NA) is equal to 0, R is returning a null value for matchid_new, thus returning a wrong list of jun_type.
for example, in my case it was giving me a list full of junctions that connect 2 known exons (97000 junctions that connect 2 known exons).
and after changing the code to :
if(length(index_NA) > 0) matchid_new <- matchid[-index_NA, ]
else {matchid_new <- matchid}
i got a list of 95000 known junctions and 2000 new alternative splicing junctions.
i am using R version 3.3.0 and customProDB version 1.10.0
thank you.
