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 <timothy.johnstone@yale.edu>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 conversati on<https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20110316="" 01="" b4dc42="" attachment.pl="">in 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 <http: timothyjohnstone.com=""/> >>>> 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]]

To me, it seems most sensible then to consider treating the end points as the ranges (width 1). I'm not sure it makes sense to map reads that are apparently aligning to introns. You can map the end points individually and then combine them back together fairly easily. Michael On Wed, Oct 2, 2013 at 11:26 AM, Tim Johnstone <timothy.johnstone@yale.edu>wrote: > I am mapping ribosome protected fragments, which may start inside one exon > and end in the following one. I'd like to convert their genomic coordinates > into transcript-based coordinates. > > When I plot the positions of the reads that result from the map function, > I see a lack of reads around each splice junction, so I'm guessing those > reads are being discarded as they're not fully contained in a given exon. > Does findOverlaps consider a read 'within' if it starts in one exon and > finishes in another? It seems like there's something obvious I'm missing. > > I guess [type="start"] is actually what I'm looking for, as otherwise > reads might be double-counted(?), but I still see no option for supplying > that to 'map'. > > Thanks > Tim > > P.S. I was previously using a function I wrote in R, which would run > findOverlaps[type=any], then take all reads that overlapped a given > transcript and convert their positions to transcript coordinates using a > 'refLoc2transcriptLoc' function I wrote. This worked for small sets, > however, it's proving far too memory- and time-inefficient for the larger > transcript sets I am now working with, so map seemed to be a good solution. > > > On Wed, Oct 2, 2013 at 1:55 PM, Michael Lawrence < > lawrence.michael@gene.com> wrote: > >> 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 < >> timothy.johnstone@yale.edu> 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 >>>>>> conversation<https: stat.ethz.ch="" pipermail="" bioconductor="" attach="" ments="" 20110316="" 01b4dc42="" attachment.pl="">in 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 <http: timothyjohnstone.com=""/> >>>>>> 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 >>> >> >> > > > -- > Timothy G. Johnstone > Yale University School of Medicine > New Haven, CT 06510 > 503-318-0962 > [[alternative HTML version deleted]]

Hi Tim, You want to coerce your reads to a GRangesList, i.e., grglist(). Then the gaps are preserved. The issue then is that the map method only accepts a GRanges for the mapping. It wouldn't be too hard to subvert the existing functionality for GRangesList. Just need to unlist the GRanges, map() it, and use relist() to get things back into the original form, if it matters. There's opportunity here for a map,GRangesList method. Michael On Thu, Oct 3, 2013 at 12:34 PM, Tim Johnstone <timothy.johnstone@yale.edu>wrote: > I think I may be going about this wrong, as my reads should not actually > align to introns. My goal is to map a set of reads (GappedAlignments) to > transcript coordinates (contained in a TranscriptDB) > > I have been coercing the GappedAlignments object to a GRanges, and > coercing the TranscriptDB to a GRangesList (using exonsBy) in order to run > map(GRanges, GRangesList). During that coercion, the GappedAlignments loses > gap information, meaning that the reads would be interpreted as overlapping > introns (whereas they are actually gapped and span exon boundaries as > expected). > > I would just map the start positions of the reads as you suggest, but I > need to preserve the read length (qwidth) information. > > How should I go about performing this mapping? > > Thanks again, and sorry for the confusion > Tim > > On Wed, Oct 2, 2013 at 4:00 PM, Michael Lawrence < > lawrence.michael@gene.com> wrote: > >> To me, it seems most sensible then to consider treating the end points as >> the ranges (width 1). I'm not sure it makes sense to map reads that are >> apparently aligning to introns. You can map the end points individually and >> then combine them back together fairly easily. >> >> Michael >> >> >> On Wed, Oct 2, 2013 at 11:26 AM, Tim Johnstone < >> timothy.johnstone@yale.edu> wrote: >> >>> I am mapping ribosome protected fragments, which may start inside one >>> exon and end in the following one. I'd like to convert their genomic >>> coordinates into transcript-based coordinates. >>> >>> When I plot the positions of the reads that result from the map >>> function, I see a lack of reads around each splice junction, so I'm >>> guessing those reads are being discarded as they're not fully contained in >>> a given exon. Does findOverlaps consider a read 'within' if it starts in >>> one exon and finishes in another? It seems like there's something obvious >>> I'm missing. >>> >>> I guess [type="start"] is actually what I'm looking for, as otherwise >>> reads might be double-counted(?), but I still see no option for supplying >>> that to 'map'. >>> >>> Thanks >>> Tim >>> >>> P.S. I was previously using a function I wrote in R, which would run >>> findOverlaps[type=any], then take all reads that overlapped a given >>> transcript and convert their positions to transcript coordinates using a >>> 'refLoc2transcriptLoc' function I wrote. This worked for small sets, >>> however, it's proving far too memory- and time-inefficient for the larger >>> transcript sets I am now working with, so map seemed to be a good solution. >>> >>> >>> On Wed, Oct 2, 2013 at 1:55 PM, Michael Lawrence < >>> lawrence.michael@gene.com> wrote: >>> >>>> 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 < >>>> timothy.johnstone@yale.edu> 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 >>>>>>>> conversation<https: stat.ethz.ch="" pipermail="" bioconductor="" atta="" chments="" 20110316="" 01b4dc42="" attachment.pl="">in 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 <http: timothyjohnstone.com=""/> >>>>>>>> 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 >>>>> >>>> >>>> >>> >>> >>> -- >>> 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]]

I think your data are sufficiently complex that you should have just a table with the read ID, range and transcript ID. Easily formed with: DataFrame(read = togroup(grl)[queryHits(m)], tx = subjectHits(m), range = ranges(m)) Michael On Thu, Oct 3, 2013 at 7:59 PM, Tim Johnstone <timothy.johnstone@yale.edu>wrote: > Unfortunately it's not that easy, my analysis won't work with the reads > being broken into multiple sub-ranges as I need to preserve their length > and make sure I'm not double-counting. It's determining which reads were > split and recombining them after the mapping that I'm not sure about. I > understand the concept behind relist(), but I'm not actually sure how to > combine that with the results of map() to recover the full gapped reads. > > Thanks for taking the time to help > > Best, > Tim > > > On Thu, Oct 3, 2013 at 7:22 PM, Michael Lawrence < > lawrence.michael@gene.com> wrote: > >> >> >> >> On Thu, Oct 3, 2013 at 4:15 PM, Tim Johnstone <timothy.johnstone@yale.edu>> > wrote: >> >>> Hi Michael, >>> >>> What should I do with the RangesMapping object in order to reconstruct >>> the reads that were split when coercing to GRanges? Thus far I cannot get >>> relist to work. >>> >>> My end goal is to have the following IRangesList (where each IRanges >>> holds all the reads that align to a transcript, and each range is a read in >>> transcript coordinates). >>> >>> >> So you are OK with a read being broken into multiple sub-ranges? The >> RangesMapping will give you the queryHits(mapping) [the indices of the read >> ranges], the subjectHits(mapping) [the transcript indices] and the >> ranges(mapping) [coordinates]. >> >> So just do something like split(ranges(m), subjectHits(m)) to get a >> RangesList like the one you want. >> >> >> >>> > refSeqReads_TxCoord >>> IRangesList of length 15759 >>> $NM_001089558 >>> IRanges of length 13 >>> start end width >>> [1] 380 400 21 >>> [2] 380 400 21 >>> [3] 380 400 21 >>> [4] 380 400 21 >>> [5] 2277 2305 29 >>> ... ... ... ... >>> [9] 2278 2306 29 >>> [10] 2278 2306 29 >>> [11] 2278 2306 29 >>> [12] 2279 2303 25 >>> [13] 2278 2306 29 >>> >>> $NM_131819 >>> IRanges of length 0 >>> >>> $NM_173228 >>> IRanges of length 4 >>> start end width >>> [1] 126 147 22 >>> [2] 126 147 22 >>> [3] 128 148 21 >>> [4] 128 148 21 >>> >>> ... >>> <15756 more elements> >>> >>> Thanks, >>> Tim >>> >>> >>> On Thu, Oct 3, 2013 at 3:42 PM, Michael Lawrence < >>> lawrence.michael@gene.com> wrote: >>> >>>> Hi Tim, >>>> >>>> You want to coerce your reads to a GRangesList, i.e., grglist(). Then >>>> the gaps are preserved. The issue then is that the map method only accepts >>>> a GRanges for the mapping. It wouldn't be too hard to subvert the existing >>>> functionality for GRangesList. Just need to unlist the GRanges, map() it, >>>> and use relist() to get things back into the original form, if it matters. >>>> There's opportunity here for a map,GRangesList method. >>>> >>>> Michael >>>> >>>> >>>> On Thu, Oct 3, 2013 at 12:34 PM, Tim Johnstone < >>>> timothy.johnstone@yale.edu> wrote: >>>> >>>>> I think I may be going about this wrong, as my reads should not >>>>> actually align to introns. My goal is to map a set of reads >>>>> (GappedAlignments) to transcript coordinates (contained in a TranscriptDB) >>>>> >>>>> I have been coercing the GappedAlignments object to a GRanges, and >>>>> coercing the TranscriptDB to a GRangesList (using exonsBy) in order to run >>>>> map(GRanges, GRangesList). During that coercion, the GappedAlignments loses >>>>> gap information, meaning that the reads would be interpreted as overlapping >>>>> introns (whereas they are actually gapped and span exon boundaries as >>>>> expected). >>>>> >>>>> I would just map the start positions of the reads as you suggest, but >>>>> I need to preserve the read length (qwidth) information. >>>>> >>>>> How should I go about performing this mapping? >>>>> >>>>> Thanks again, and sorry for the confusion >>>>> Tim >>>>> >>>>> On Wed, Oct 2, 2013 at 4:00 PM, Michael Lawrence < >>>>> lawrence.michael@gene.com> wrote: >>>>> >>>>>> To me, it seems most sensible then to consider treating the end >>>>>> points as the ranges (width 1). I'm not sure it makes sense to map reads >>>>>> that are apparently aligning to introns. You can map the end points >>>>>> individually and then combine them back together fairly easily. >>>>>> >>>>>> Michael >>>>>> >>>>>> >>>>>> On Wed, Oct 2, 2013 at 11:26 AM, Tim Johnstone < >>>>>> timothy.johnstone@yale.edu> wrote: >>>>>> >>>>>>> I am mapping ribosome protected fragments, which may start inside >>>>>>> one exon and end in the following one. I'd like to convert their genomic >>>>>>> coordinates into transcript-based coordinates. >>>>>>> >>>>>>> When I plot the positions of the reads that result from the map >>>>>>> function, I see a lack of reads around each splice junction, so I'm >>>>>>> guessing those reads are being discarded as they're not fully contained in >>>>>>> a given exon. Does findOverlaps consider a read 'within' if it starts in >>>>>>> one exon and finishes in another? It seems like there's something obvious >>>>>>> I'm missing. >>>>>>> >>>>>>> I guess [type="start"] is actually what I'm looking for, as >>>>>>> otherwise reads might be double-counted(?), but I still see no option for >>>>>>> supplying that to 'map'. >>>>>>> >>>>>>> Thanks >>>>>>> Tim >>>>>>> >>>>>>> P.S. I was previously using a function I wrote in R, which would run >>>>>>> findOverlaps[type=any], then take all reads that overlapped a given >>>>>>> transcript and convert their positions to transcript coordinates using a >>>>>>> 'refLoc2transcriptLoc' function I wrote. This worked for small sets, >>>>>>> however, it's proving far too memory- and time-inefficient for the larger >>>>>>> transcript sets I am now working with, so map seemed to be a good solution. >>>>>>> >>>>>>> >>>>>>> On Wed, Oct 2, 2013 at 1:55 PM, Michael Lawrence < >>>>>>> lawrence.michael@gene.com> wrote: >>>>>>> >>>>>>>> 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 < >>>>>>>> timothy.johnstone@yale.edu> 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 conversation<https: stat.ethz.ch="" pipermail="" biocondu="" ctor="" attachments="" 20110316="" 01b4dc42="" attachment.pl="">in 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 <http: timothyjohnstone.com=""/> >>>>>>>>>>>> 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 >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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 >>> >> >> > > > -- > Timothy G. Johnstone > Yale University School of Medicine > New Haven, CT 06510 > 503-318-0962 > [[alternative HTML version deleted]]