thanks - much tidier than my way.
Janet
On Jun 23, 2011, at 2:08 AM, Martin Morgan wrote:
> On 06/22/2011 05:33 PM, Janet Young wrote:
>> Hi again,
>>
>> Thanks, Michael - looking forward to seqselect on GRanges being implemented,
>> if possible. Getting a little further through my old code, brings up another
>> related request.
>>
>> Here are some slightly different example ranges:
>> myGR<-
>> GRanges(seqnames=c("chr1","chr2","chr2"),ranges=IRanges(start=c(25,40,60),end=c(35,45,65))
>> )
>> myRD<-
>> RangedData(space=c("chr1","chr2","chr2"),IRanges(start=c(25,40,60),end=c(35,45,65))
>> )
>>
>> And I had previously been using this command:
>> restrict(ranges(myRD), 30,50)
>> I'm doing that because I'm interested in ranges within the same region on
>> every single "chromosome". With my real data, they spaces/seqnames are not
>> chromosomes, they're promoter regions centered around the transcription
>> start site, and I want to take various equivalent sub-portions of the whole
>> set of promoters)
>>
>> I can't get "restrict" to work on the GRanges object at the moment (even if
>> I try that same coercion first):
>> restrict( myGR , 30,50)
>> Error in function (classes, fdef, mtable) :
>> unable to find an inherited method for function "restrict", for
>> signature "GRanges"
>>
>> restrict( as(myGR,"RangesList") , 30,50)
>> Error in sapply(listData, function(Xi) extends(class(Xi),
>> elementTypeX)) :
>> error in evaluating the argument 'X' in selecting a method for
>> function 'sapply': Error in .CompressedList.list.subscript(X = X, INDEX =
>> seq_len(length(X)), :
>> invalid output element of class "IRanges"
>>
>> It would be great if restrict could work directly in the same way as it did
>> for RangedData. In the meantime I can probably figure out a way to do it
>> with lapply.
>
>
> or
>
> rng <- restrict(ranges(gr), 30, 50, keep.all.ranges=TRUE)
> ranges(gr) <- rng
> gr[width(gr) != 0]
>
> (and similarly for GRangesList).
>
> Martin
>
>> thanks,
>>
>> Janet
>>
>>
>>
>> On Jun 22, 2011, at 4:19 PM, Michael Lawrence wrote:
>>
>>> Hi,
>>>
>>> There is already a coercion from GRanges to RangesList, i.e., as(gr,
>>> "RangesList"). That said, seqselect() should have a method for GRanges, if
>>> possible.
>>>
>>> Michael
>>>
>>> On Wed, Jun 22, 2011 at 4:15 PM, Janet Young<jayo...@fhcrc.org> wrote:
>>> Hi again,
>>>
>>> A further note - the workaround I first emailed only works when there's one
>>> range per chromosome. I have a better workaround now - the coercion looks
>>> like this instead:
>>>
>>> convertGRangesToCompressedIRangesList<- function (myGRobject) {
>>> myGR_convert<- split(myGRobject, seqnames(myGRobject) )
>>> names(myGR_convert)<- unlist(lapply(myGR_convert, function(x) {
>>> as.character(seqnames(x))[1] }))
>>>
>>> myGR_convert<- lapply(myGR_convert, ranges )
>>> class(myGR_convert)<- "CompressedIRangesList"
>>> myGR_convert
>>> }
>>>
>>> Janet
>>>
>>>
>>>
>>> Begin forwarded message:
>>>
>>>> From: Janet Young<jayo...@fhcrc.org>
>>>> Date: June 22, 2011 4:01:03 PM PDT
>>>> To: Bioc-sig-sequencing@r-project.org
>>>> Subject: seqselect using GRanges object on multiple chromosomes
>>>>
>>>> Hi there,
>>>>
>>>> I'm updating some of my older code - I was previously storing regions of
>>>> interest as RangedData but now I'm switching to GRanges. I'm running into
>>>> a little trouble with seqselect - I've found a workaround but wanted to
>>>> suggest extending seqselect so it can work with GRanges objects directly.
>>>>
>>>> I have some scores for each base-pair I've stored as a SimpleRleList
>>>> object. I want to use GRanges object with seqselect to pull out scores
>>>> from my regions of interest, but to make that work I first have to do an
>>>> odd (and slightly wrong-looking, to me) coercion of my GRanges object to a
>>>> CompressedIRangesList.
>>>>
>>>> I think the code below explains all (?).
>>>>
>>>> thanks very much,
>>>>
>>>> Janet
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> library(GenomicRanges)
>>>> Loading required package: IRanges
>>>>
>>>> Attaching package: 'IRanges'
>>>>
>>>> The following object(s) are masked from 'package:base':
>>>>
>>>> cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin,
>>>> pmin.int, rbind, rep.int, setdiff, table, union
>>>>
>>>>>
>>>>> ### make some scores objects, for single chromosomes, or across several
>>>>> chrs
>>>>> tempscores<- Rle(1:20)
>>>>> tempscores2<- Rle(101:120)
>>>>> allscores<- RleList(chr1=tempscores,chr2=tempscores2) # yields a
>>>>> SimpleRleList
>>>>>
>>>>> ## make some ranges objects
>>>>> myIR<- IRanges(start=3,end=5)
>>>>> myGR<- GRanges(seqnames=c("chr1","chr2"),ranges=IRanges(start=3,end=5))
>>>>> myRD<- RangedData(space=c("chr1","chr2"),IRanges(start=c(3,3),end=c(5,5))
>>>>> )
>>>>>
>>>>>
>>>>> ### test seqselect:
>>>>> seqselect(tempscores,myIR) #works
>>>> 'integer' Rle of length 3 with 3 runs
>>>> Lengths: 1 1 1
>>>> Values : 3 4 5
>>>>> seqselect(allscores,myGR) # doesn't work
>>>> Error in seqselect(allscores, myGR) : unrecognized 'start' type
>>>>> seqselect(allscores,myRD) # doesn't work
>>>> Error in seqselect(allscores, myRD) : unrecognized 'start' type
>>>>>
>>>>> seqselect(allscores,ranges(myRD)) # works. ranges(myRD) is a
>>>>> CompressedIRangesList
>>>> SimpleRleList of length 2
>>>> $chr1
>>>> 'integer' Rle of length 3 with 3 runs
>>>> Lengths: 1 1 1
>>>> Values : 3 4 5
>>>>
>>>> $chr2
>>>> 'integer' Rle of length 3 with 3 runs
>>>> Lengths: 1 1 1
>>>> Values : 103 104 105
>>>>
>>>>>
>>>>> seqselect(allscores,ranges(myGR)) # doesn't work
>>>> Error in .bracket.Index(start, length(x), names(x), asRanges = TRUE) :
>>>> range index out of bounds
>>>>> seqselect(allscores,split(myGR)) # doesn't work
>>>> Error in seqselect(allscores, split(myGR)) : unrecognized 'start' type
>>>>>
>>>>> #### coerce myGR to something that looks a bit like a
>>>>> CompressedIRangesList
>>>>> myGR_convert<- split(myGR)
>>>>> names(myGR_convert)<- names(seqlengths(myGR_convert))
>>>>> myGR_convert<- lapply(myGR_convert, ranges )
>>>>> class(myGR_convert)<- "CompressedIRangesList"
>>>>>
>>>>>
>>>>> seqselect(allscores,myGR_convert) # works
>>>> SimpleRleList of length 2
>>>> $chr1
>>>> 'integer' Rle of length 3 with 3 runs
>>>> Lengths: 1 1 1
>>>> Values : 3 4 5
>>>>
>>>> $chr2
>>>> 'integer' Rle of length 3 with 3 runs
>>>> Lengths: 1 1 1
>>>> Values : 103 104 105
>>>>
>>>>>
>>>>> sessionInfo()
>>>> R version 2.13.0 (2011-04-13)
>>>> 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] GenomicRanges_1.4.6 IRanges_1.10.4
>>>>
>>>>
>>>
>>> _______________________________________________
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>>> Bioc-sig-sequencing@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>
>>
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>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
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