[Bioc-sig-seq] Consolidating RangedData
Ivan Gregoretti
ivangreg at gmail.com
Thu Jan 6 17:21:42 CET 2011
I assumed that RangedDataList was the same as "list of RangedData".
at the moment I can't coerce one into the other:
as(LargeListOfSmallRangedData,'RangedDataList')
Error in as(LargeListOfSmallRangedData, "RangedDataList") :
no method or default for coercing "list" to "RangedDataList"
so, I will have to stick to do.call().
Thank you,
Ivan
On Thu, Jan 6, 2011 at 10:08 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
>
>
> On Thu, Jan 6, 2011 at 6:46 AM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>>
>> Hi Michael,
>>
>> Sorry I couldn't provide more details yesterday. When I saw your post
>> I was logged out from the server and already on my way out of the
>> office.
>>
>> This is my experience with stack(). Please see below.
>>
>> Thank you,
>>
>> Ivan
>>
>>
>> ### load relevant libraries
>> library(Biostrings)
>> library(BSgenome.Mmusculus.UCSC.mm9)
>>
>> ### define a subset of chromosomes
>> someChromosomes <- c('chr1', 'chr2', 'chr3', 'chr4', 'chr5',
>> 'chr6', 'chr7', 'chr8', 'chr9', 'chr10',
>> 'chr11', 'chr12', 'chr13', 'chr14', 'chr15',
>> 'chr16', 'chr17', 'chr18', 'chr19',
>> 'chrX')
>>
>> ### generate a series of ranges at the end of the chromosomes
>> LargeListOfSmallRangedData <- lapply(someChromosomes,
>>
>>
>> function(x){RangedData(ranges=IRanges(start=seq(length(Mmusculus[[x]])-500+1,
>>
>> length(Mmusculus[[x]]),
>>
>> 100),
>>
>> width=100),
>> space=x,
>>
>> distance=seq(500-100,0,-100))})
>>
>> ### Peak at the first 2 elements of the list above
>> LargeListOfSmallRangedData[c(1,2)]
>>
>
> This needs to be a RangedDataList not a list of RangedData. And better use
> the latest IRanges devel, otherwise I think it's broken.
>
>>
>> ### Try to consolidate using stack(). Here is the error message
>> bigRangedData <- stack(LargeListOfSmallRangedData, indName='space')
>>
>> Error in rep.int(names(x), lapply(x, length)) :
>> unimplemented type 'NULL' in 'rep2'
>>
>> ### machine and OS information
>> sessionInfo()
>>
>> R version 2.13.0 Under development (unstable) (2010-12-02 r53747)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] BSgenome.Mmusculus.UCSC.mm9_1.3.17 BSgenome_1.19.2
>> [3] GenomicRanges_1.3.7 Biostrings_2.19.2
>> [5] IRanges_1.9.17
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.11.7
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Jan 5, 2011 at 5:11 PM, Michael Lawrence
>> <lawrence.michael at gene.com> wrote:
>> > That's the correct basic usage, but how about an error message or a
>> > little
>> > more context?
>> >
>> > On Wed, Jan 5, 2011 at 2:08 PM, Ivan Gregoretti <ivangreg at gmail.com>
>> > wrote:
>> >>
>> >> I tried to use it to the best of my understanding:
>> >>
>> >> stack(LargeListOfSmallRangedData, indName='space')
>> >>
>> >> I think that the failure is due to misuse from my part rather than a
>> >> bug.
>> >>
>> >> Ivan
>> >>
>> >>
>> >>
>> >>
>> >> On Wed, Jan 5, 2011 at 4:51 PM, Michael Lawrence
>> >> <lawrence.michael at gene.com> wrote:
>> >> > Well it would be good to see what you tried. I think there are some
>> >> > critical
>> >> > bug fixes to stack in devel, but not release, so I would try with
>> >> > devel.
>> >> >
>> >> > Michael
>> >> >
>> >> > On Wed, Jan 5, 2011 at 1:13 PM, Ivan Gregoretti <ivangreg at gmail.com>
>> >> > wrote:
>> >> >>
>> >> >> Hi Michael,
>> >> >>
>> >> >> Actually, I tried consolidating the list with stack() but I failed.
>> >> >> Perhaps there is no need to change anything but only show how the
>> >> >> consolidation is done with stack().
>> >> >>
>> >> >> Would you mind showing it for the record?
>> >> >>
>> >> >> Thank you,
>> >> >>
>> >> >> Ivan
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> On Wed, Jan 5, 2011 at 4:05 PM, Michael Lawrence
>> >> >> <lawrence.michael at gene.com> wrote:
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Jan 5, 2011 at 12:45 PM, Ivan Gregoretti
>> >> >> > <ivangreg at gmail.com>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> It works. Thanks, Martin.
>> >> >> >>
>> >> >> >> It would be nice to have a pointer to this functionality in the
>> >> >> >> documentation. For instance, when I do ?RangedData, I can see a
>> >> >> >> RangedData constructor and coercion options. However,
>> >> >> >> ?RangedDataList
>> >> >> >> reports its constructor but no coercion.
>> >> >> >>
>> >> >> >
>> >> >> > It's not a coercion in the strict sense. The rbind method is
>> >> >> > documented
>> >> >> > for
>> >> >> > RangedData. Also, RangedDataList has a stack method for rbind'ing
>> >> >> > them
>> >> >> > and
>> >> >> > adding a factor column indicating the source of each record. The
>> >> >> > "unlist"
>> >> >> > method on RangedDataList is a bit strange: it does a do.call(c,
>> >> >> > list)
>> >> >> > instead of do.call(rbind, list). I'm thinking about changing that.
>> >> >> >
>> >> >> > Michael
>> >> >> >
>> >> >> >>
>> >> >> >> Again, thank you.
>> >> >> >>
>> >> >> >> Ivan
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Jan 5, 2011 at 3:23 PM, Martin Morgan
>> >> >> >> <mtmorgan at fhcrc.org>
>> >> >> >> wrote:
>> >> >> >> > On 01/05/2011 12:12 PM, Ivan Gregoretti wrote:
>> >> >> >> >> Hello BioC listers,
>> >> >> >> >>
>> >> >> >> >> Is there a function that will take a list of RangedData
>> >> >> >> >> instances
>> >> >> >> >> and
>> >> >> >> >> consolidate them into a large RangedData instance?
>> >> >> >> >
>> >> >> >> > do.call(rbind, LargeListOfSmallRangedData)
>> >> >> >> >
>> >> >> >> > ?
>> >> >> >> > Martin
>> >> >> >> >>
>> >> >> >> >> I'm looking for this:
>> >> >> >> >>
>> >> >> >> >> bigRangedData <- someFunction( LargeListOfSmallRangedData )
>> >> >> >> >>
>> >> >> >> >> Thank you,
>> >> >> >> >>
>> >> >> >> >> Ivan
>> >> >> >> >>
>> >> >> >> >> _______________________________________________
>> >> >> >> >> Bioc-sig-sequencing mailing list
>> >> >> >> >> Bioc-sig-sequencing at r-project.org
>> >> >> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Computational Biology
>> >> >> >> > Fred Hutchinson Cancer Research Center
>> >> >> >> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>> >> >> >> >
>> >> >> >> > Location: M1-B861
>> >> >> >> > Telephone: 206 667-2793
>> >> >> >> >
>> >> >> >>
>> >> >> >> _______________________________________________
>> >> >> >> Bioc-sig-sequencing mailing list
>> >> >> >> Bioc-sig-sequencing at r-project.org
>> >> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>> >> >> >
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>
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