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lcolladotor / derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
http://lcolladotor.github.io/derfinder
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bumphunter as import #3

Closed mikelove closed 10 years ago

mikelove commented 10 years ago

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

jtleek commented 10 years ago

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.

mikelove commented 10 years ago

sure, I'm forking now.

lcolladotor commented 10 years ago

Fixed by Mike Love in 78b70658b35fb30dc12b79237d68ef1710b5b712 Note that bumphunter::annotateNearest() uses IRanges::distance() so 2592e8d69b5c07c8f7674abd93e5dbb9eefbb39b 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.

lcolladotor commented 10 years ago

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.