bumphunter as import

[Michael Love]

hi,

as you have the code in analyzeChr():

 if(!is.null(regions$regions) & runAnnotation) {
                library("bumphunter")
                annotation <- annotateNearest(regions$regions, subject)
        } else {
                annotation <- NULL
        }  

I would suggest adding bumphunter to the Import field in DESCRIPTION

best,

Mike

[Jeff L.]

If you want to add a pull request here too I think that would be great. I can do them myself, but it would be a huge help if you will.

[Michael Love]

sure, I'm forking now.

[Leonardo Collado-Torres]

Fixed by Mike Love in 78b7065 Note that bumphunter::annotateNearest() uses IRanges::distance() so 2592e8d takes that into account.

However, there is currently an error as described in https://stat.ethz.ch/pipermail/bioc-devel/2013-November/004958.html Waiting for help from BioC experts.

[Leonardo Collado-Torres]

Found a solution to this problem by modifying the NAMESPACE of the bumphunter package as I reported here https://stat.ethz.ch/pipermail/bioc-devel/2013-November/004967.html

Currently waiting for these changes to be implemented on the release version of bumphunter.