Hi Julian, Michael,
Alternatively a trick is to use the outer mcols of the GRangesList
object. If the experimental metadata of each GRanges has the same
structure/fields, and those fields contain single values:
library(GenomicRanges)
gr1 <- GRanges()
metadata(gr1) = list(a="1", b="hello")
Related to the storage of a list inside a DataFrame (as a column),
I found 2 issues:
df <- DataFrame(A=I(list(a=1:3, b="BB")))
1. The name of the col is not as specified:
> df
DataFrame with 2 rows and 1 column
X
1
2
2. rbind() doesn't
Hi Michael,
I can't reproduce this:
> library(GenomicRanges)
> chrs <- c(chr1=20, chr2=20)
> grA <- GRanges("chr1", IRanges(1,10), strand="*", seqlengths=chrs)
> grB <- GRanges("chr2", IRanges(11,15), strand="*", seqlengths=chrs)
> setdiff(grA, grB)
GRanges with 1 range and 0 metadat
Hi Michael,
Thanks, using 'GenomicRangesList' instead of 'GRangesList' essentially
solves my issues. Could you please add a small note to the
documentation that mentions the different behaviors for the two classes?
Best wishes
Julian
On 09/03/2013 03:34 PM, Michael Lawrence wrote:
If the
If the number of GRanges is small (not thousands), and you don't need the
semantic of treating each GRanges as a "compound range", then use
GenomicRangesList(). It's a SimpleList, so metadata should be preserved.
It's the data structure for storing per-sample GRanges.
Michael
On Tue, Sep 3, 2013
Yep, Michael will send a pull request within the next few weeks.
Michael
On Tue, Sep 3, 2013 at 6:07 AM, Hahne, Florian
wrote:
> Great, thanks for the feedback. I will give it a try asap.
>
> Am Sep 3, 2013 um 15:03 schrieb "Martin Morgan" :
>
> > On 09/03/2013 05:25 AM, Hahne, Florian wrote:
>
Great, thanks for the feedback. I will give it a try asap.
Am Sep 3, 2013 um 15:03 schrieb "Martin Morgan" :
> On 09/03/2013 05:25 AM, Hahne, Florian wrote:
>> Hi List, Martin,
>> I just wanted to quickly ask about the status of the BiocParallel package and
>> the cluster support in particular. I
On 09/03/2013 05:25 AM, Hahne, Florian wrote:
Hi List, Martin,
I just wanted to quickly ask about the status of the BiocParallel package and
the cluster support in particular. Is this project finished? And are there plans
to having BiocParallel as a proper package again, or will it remain a GIT
Hi List, Martin,
I just wanted to quickly ask about the status of the BiocParallel package and
the cluster support in particular. Is this project finished? And are there
plans to having BiocParallel as a proper package again, or will it remain a GIT
project?
Florian
[[alternative HTML v
Hi Michael,
The use case is storing experimental metadata togther with a GRanges
object that does not fit the tabular structure of a GRange. And at a
later stage, storing multiple of these annotated GRanges objects
together as a list/GRangesList.
Best wishes
Julian
This second case is ex
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