[Bioc-sig-seq] rtracklayer and import()ing into GRanges
Ivan Gregoretti
ivangreg at gmail.com
Tue Aug 10 21:13:01 CEST 2010
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 <paboyoun at fhcrc.org> 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 <paboyoun at fhcrc.org> 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 <paboyoun at fhcrc.org>
>> 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 <paboyoun at fhcrc.org>
>>> 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<ivangreg at gmail.com>
>>>>> 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
>>>>>> Bioc-sig-sequencing at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>>>
>>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
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>>>>>
>>>>
>>>
>>>
>>
>>
>
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