Hi Patrick, I tried the new GRanges functionality of import() and it works great.
That leads me to a related question. How do you remove, say, the field "score"? In the past, when I loaded my BED features into a RangedData object called A, removing the field "score" was as simple as: A$score <- NULL Now that A is a GRanges object, how do I do the same? Thank you, Ivan On Thu, Aug 5, 2010 at 8:06 PM, Patrick Aboyoun <[email protected]> wrote: > I just checked in a patch to rtracklayer version 1.9.6 into BioC 2.7 that > added asRangedData arguments to all of the import methods except import.bw > as well as to the GenomicData function. When asRangedData = FALSE, these > import methods will produce GRanges objects. I didn't optimize any of the > code yet, so there may be another rev tomorrow with some tweaks to the > import code at the R level. Here is are some examples: > >> library(rtracklayer) >> bedfilepath <- system.file("tests", "test.bed", package = "rtracklayer") >> import(bedfilepath, asRangedData = FALSE) > GRanges with 9 ranges and 5 elementMetadata values > seqnames ranges strand | name score > thickStart > <Rle> <IRanges> <Rle> | <character> <numeric> > <integer> > [1] chr7 [127471197, 127472363] + | Pos1 0 > 127471196 > [2] chr7 [127472364, 127473530] + | Pos2 0 > 127472363 > [3] chr7 [127473531, 127474697] + | Pos3 0 > 127473530 > [4] chr7 [127474698, 127475864] + | Pos4 0 > 127474697 > [5] chr7 [127475865, 127477031] - | Neg1 0 > 127475864 > [6] chr7 [127477032, 127478198] - | Neg2 0 > 127477031 > [7] chr7 [127478199, 127479365] - | Neg3 0 > 127478198 > [8] chr7 [127479366, 127480532] + | Pos5 0 > 127479365 > [9] chr7 [127480533, 127481699] - | Neg4 0 > 127480532 > thickEnd itemRgb > <integer> <character> > [1] 127472363 #FF0000 > [2] 127473530 #FF0000 > [3] 127474697 #FF0000 > [4] 127475864 #FF0000 > [5] 127477031 #0000FF > [6] 127478198 #0000FF > [7] 127479365 #0000FF > [8] 127480532 #FF0000 > [9] 127481699 #0000FF > > seqlengths > chr7 > NA >> bed15filepath <- system.file("tests", "test.bed15", package = >> "rtracklayer") >> import(bed15filepath, asRangedData = FALSE) > GRanges with 2 ranges and 13 elementMetadata values > seqnames ranges strand | name score > thickStart > <Rle> <IRanges> <Rle> | <character> <numeric> > <integer> > [1] chr1 [159639973, 159640031] - | 2440848 500 > 159639972 > [2] chr1 [159640162, 159640190] - | 2440849 500 > 159640161 > thickEnd itemRgb blockCount blockSizes blockStarts breast_A > <integer> <character> <integer> <character> <character> <numeric> > [1] 159640031 NA 1 59, 0, 0.593 > [2] 159640190 NA 1 29, 0, -0.906 > breast_B breast_C cerebellum_A cerebellum_B > <numeric> <numeric> <numeric> <numeric> > [1] 1.196 -0.190 -1.088 0.093 > [2] -1.247 0.111 -0.515 -0.057 > > seqlengths > chr1 > NA >> sessionInfo() > R version 2.12.0 Under development (unstable) (2010-08-01 r52659) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.9.6 RCurl_1.4-3 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.9.0 Biostrings_2.17.27 BSgenome_1.17.6 > [4] GenomicRanges_1.1.20 IRanges_1.7.15 tools_2.12.0 > [7] XML_3.1-0 > > > Patrick > > > On 8/5/10 1:11 PM, Michael Lawrence wrote: > > On Thu, Aug 5, 2010 at 10:45 AM, Patrick Aboyoun <[email protected]> wrote: >> >> Michael, >> I just made a minor check-in to rtracklayer where I replaced use of >> Biobase:listLen with IRanges::elementLenghts in an effort to minimize the >> impact of Biobase on the sequence package stack. >> > > Ok. It looks like elementLengths has been optimized since the last time I > looked. > > >> >> Before I start the boulder rolling, how should I reconcile the UCSCData >> class with the GRanges class? Once I have that sorted I can make changes to >> import.bed and import.wig as well. >> > > Well, eventually we'll want to stick the track line information on to > GRanges. Could be done via a subclass like with UCSCData. metadata() is > another option. I do actually use the subclass for dispatch purposes, pretty > printing, etc. For right now though, the extra information could just be > dropped if the user requests a GRanges. > >> >> I originally named the argument asRangedData in the BSgenome methods to >> reinforce that RangedData output is not intended to be the default and >> conceptually the user is making an extra effort to produce a RangedData >> object. >> >> >> Patrick >> >> >> On 8/5/10 4:32 AM, Michael Lawrence wrote: >> >> Makes sense. But why not make it asGRanges, which is shorter? Please go >> ahead and check in your work so far. >> >> Thanks a lot, >> Michael >> >> On Thu, Aug 5, 2010 at 12:51 AM, Patrick Aboyoun <[email protected]> >> wrote: >>> >>> Michael, >>> Breaking this down to two issues: >>> >>> Filtering >>> Martin has been working on improving filtering in the ShortRead package >>> to move from a read all then filter data to a block processing based >>> filtering methodology. Lessons learned there can be brought to rtracklayer >>> for large bed files and the like. >>> >>> import() output class >>> Keeping the same API and just switching the import methods from producing >>> RangedData (or UCSCData) output to GRanges output will break backward >>> compatibility because the RangedData API is not wholly applicable to GRanges >>> objects. I would not recommend this course since a number of packages in >>> BioC and scripts in the wild expect the import methods to produce a >>> RangedData (or UCSCData) object. An additional argument is not that onerous >>> and can be fazed out over the course of two or three releases (1 - 1.5 >>> years). Another alternative is to add a new import function (read.GRanges?) >>> to rtracklayer that shares the same infrastructure as the existing import >>> methods. >>> >>> I have a local copy of rtracklayer where I added a new asRangedData flag >>> to the GenomicData function and import.gff* methods. I'll sit on this for >>> now since these changes didn't take a lot of work. This is one of the >>> situations where the managing the life cycle of the function specs is >>> trickier than making the desired code changes. >>> >>> >>> Cheers, >>> Patrick >>> >>> >>> On 8/4/10 8:24 PM, Michael Lawrence wrote: >>> >>> This might work, but it seems like an expensive optimization in that it >>> changes a lot of the API. If someone cannot make a single copy of the data, >>> it's unlikely that they're even going to be able to get to GenomicData() or >>> manipulate it later. Perhaps the coercion function needs some simple tweaks? >>> The filter support would definitely help. I'd rather keep things simple and >>> return a single type, and GRanges sounds most appropriate. >>> >>> But I'm open to suggestions and further argument. >>> >>> Michael >>> >>> On Wed, Aug 4, 2010 at 2:05 PM, Patrick Aboyoun <[email protected]> >>> wrote: >>>> >>>> Michael, >>>> How integrated would you like to see the GRanges class in rtracklayer? >>>> The rtracklayer::GenomicData constructor is the master instantiator. I >>>> would >>>> like to add an asRangedData = TRUE (default) argument to the GenomicData >>>> function and push it all the way up through the import functions where when >>>> the user sets asRangedData = FALSE, the GenomicData function would create a >>>> GRanges object. This is what we did with the >>>> {matchPWM,vmatchPattern,vmatchPDict},BSgenome-methods in the BSgenome >>>> package and it as good a solution as any. This is a straight-forward change >>>> and wouldn't take too long to complete. >>>> >>>> >>>> Patrick >>>> >>>> >>>> On 8/4/10 12:56 PM, Michael Lawrence wrote: >>>>> >>>>> GRanges support is definitely on the TODO list. Filters are a good idea >>>>> and >>>>> also on the TODO list, possibly with a chunk size parameter to enable >>>>> chunk >>>>> processing. >>>>> >>>>> I'd love to have the GRanges stuff at least done by the next release. >>>>> Patches welcome, of course :) >>>>> >>>>> Michael >>>>> >>>>> On Wed, Aug 4, 2010 at 8:08 AM, Ivan Gregoretti<[email protected]> >>>>> wrote: >>>>> >>>>> >>>>>> >>>>>> Hello Michael and everyone, >>>>>> >>>>>> Would you please consider adding to import() the capacity to generate >>>>>> a GRanges object rather than the default RangedData object? >>>>>> >>>>>> Also, >>>>>> >>>>>> Wouldn't it be great to be able to import() with filters just like >>>>>> with readAligned()? >>>>>> >>>>>> >>>>>> >>>>>> Justification >>>>>> >>>>>> GRanges is a biology-aware container. When importing large BEDs into >>>>>> R, the current workflow involves creating RangedData first and then >>>>>> converting to GRanges. >>>>>> >>>>>> If the BEDs are really big, holding both objects in memory at any >>>>>> point in time is a hardware challenge. >>>>>> >>>>>> The capacity to filter the input would help in this case and in >>>>>> general it would provide an increase in efficiency. >>>>>> >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Ivan >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Ivan Gregoretti, PhD >>>>>> National Institute of Diabetes and Digestive and Kidney Diseases >>>>>> National Institutes of Health >>>>>> 5 Memorial Dr, Building 5, Room 205. >>>>>> Bethesda, MD 20892. USA. >>>>>> Phone: 1-301-496-1016 and 1-301-496-1592 >>>>>> Fax: 1-301-496-9878 >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-sig-sequencing mailing list >>>>>> [email protected] >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>>>>> >>>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioc-sig-sequencing mailing list >>>>> [email protected] >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>>>> >>>> >>> >>> >> >> > > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
