Open lukauskas opened 3 years ago
Hi @lukauskas this is a very good question, and I think this will be relevant to other users as well. proActiv is now hosted on Bioconductor (you can install the latest version here: https://www.bioconductor.org/packages/release/bioc/html/proActiv.html). Would you mind posting this question to the Bioconductor forum? https://support.bioconductor.org/ We will respond there so others can easily find this.
Hi again,
While investigating the
proActiv
results for my sample dataset I came across the fact that many genes do not have a "Major" promoter, yet they tend to have multiple Minor promoters.This was a bit unexpected as example workflow states the following (emphasis mine):
I now realise that this is related to the other statement described in limitations section:
Which makes sense. Looking at the source code, I believe this limitation is implemented as
internalPromoter
column in the output ofproActiv
.In the actual implementation, specifically these lines, the "Major/Minor" classification is assigned before filtering out the internal promoters though.
In cases where an
internalPromoter
has higher activity than any non internal promoter, this would result this internal promoter being assigned theMajor
tag in the code. This assignment would be overwritten withNA
immediately, but no other promoter being selected asMajor
leaving onlyMinor
promoters andNA
s.Minor
promoters that are notinternalPromoter
be assigned theMajor
label in these cases?