On Thu, Jan 6, 2011 at 6:46 AM, Ivan Gregoretti <[email protected]> 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
> <[email protected]> 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 <[email protected]>
> 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
> >> <[email protected]> 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 <[email protected]>
> >> > 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
> >> >> <[email protected]> wrote:
> >> >> >
> >> >> >
> >> >> > On Wed, Jan 5, 2011 at 12:45 PM, Ivan Gregoretti <
> [email protected]>
> >> >> > 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 <[email protected]
> >
> >> >> >> 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
> >> >> >> >> [email protected]
> >> >> >> >> 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
> >> >> >> >
> >> >> >>
> >> >> >> _______________________________________________
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> >> >> >> [email protected]
> >> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >> >> >
> >> >> >
> >> >
> >> >
> >
> >
>
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