What do you want to happen in that case? Those reads would be outside the annotated transcript. On Wed, Oct 2, 2013 at 10:48 AM, Tim Johnstone wrote: > Thanks for your response! > > From what I can see, map calls 'findOverlaps' using [type="within"]. Is > it possible to supply an argument to 'map' such that it will call > findOverlaps with [type="any"]? I am running map(GappedAlignments, > GRangesList), where the GRangesList is a list of exons, and I need to > include reads that overlap the exons at any point, but it currently looks > like I'm not capturing the reads at intron-exon boundaries as they don't > fully overlap. > > Thanks, > Tim J. > > > On Tue, Sep 17, 2013 at 1:06 PM, Michael Lawrence < > lawrence.michael@gene.com> wrote: > >> There is a method on the map generic in GenomicRanges that will do this >> given a GRanges of genomic/global coordinates, and a GRangesList defining >> transcripts or any other type of compound region. The returned >> RangesMapping object tells you the hits (which overlapped which) and for >> each hit the local coordinates. >> >> Michael >> >> >> On Tue, Sep 17, 2013 at 9:33 AM, Tim Johnstone < >> timothy.johnstone@yale.edu> wrote: >> >>> To add to my previous email, I just found the refLocsToLocalLocs >>> function in the VariantAnnotation package you co-authored, but need to >>> convert single positions that align anywhere in the transcript, rather than >>> ranges that align to just the coding region. It looks like it may be >>> possible to get this behavior by supplying exonsByTx as both the second and >>> the third arguments, but let me know if there is an easier way. >>> >>> Best, >>> Tim Johnstone >>> >>> >>> On Tue, Sep 17, 2013 at 12:19 PM, Tim Johnstone < >>> timothy.johnstone@yale.edu> wrote: >>> >>>> Dear Michael, >>>> >>>> I am working with the GenomicRanges bioconductor package, and I've been >>>> trying to find a way to convert a set of locations in genomic coordinates >>>> to transcript coordinates. I found an old mailing list conversationin which you indicated you were planning to implement that function >>>> (refLocs2TranscriptLocs or globalToLocal) in GenomicRanges/GenomicFeatures, >>>> but in looking through the source code I can't find it. Was this function >>>> ever implemented, and if so, would it be possible for you to send it to me? >>>> >>>> Thanks! >>>> Tim Johnstone >>>> >>>> -- >>>> Timothy G. Johnstone >>>> Yale University School of Medicine >>>> New Haven, CT 06510 >>>> 503-318-0962 >>>> >>> >>> >>> >>> -- >>> Timothy G. Johnstone >>> Yale University School of Medicine >>> New Haven, CT 06510 >>> 503-318-0962 >>> >> >> > > > -- > Timothy G. Johnstone > Yale University School of Medicine > New Haven, CT 06510 > 503-318-0962 > [[alternative HTML version deleted]]