[Bioc-sig-seq] Consolidating RangedData

[Ivan Gregoretti]

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
>> >> >>
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>> >> >
>> >> >
>> >> > --
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>> >> >
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>
>