Re: [Bioc-devel] 'GRangesList' does not keep metadata of items

2013-09-03 Thread Julian Gehring
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

[Bioc-devel] BiocParallel status

2013-09-03 Thread Hahne, Florian
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

Re: [Bioc-devel] BiocParallel status

2013-09-03 Thread 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. Is this project finished? And are there plans to having BiocParallel as a proper package again, or will it remain a GIT

Re: [Bioc-devel] BiocParallel status

2013-09-03 Thread Hahne, Florian
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

Re: [Bioc-devel] BiocParallel status

2013-09-03 Thread Michael Lawrence
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: >

Re: [Bioc-devel] 'GRangesList' does not keep metadata of items

2013-09-03 Thread Michael Lawrence
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

Re: [Bioc-devel] 'GRangesList' does not keep metadata of items

2013-09-03 Thread Julian Gehring
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

Re: [Bioc-devel] setdiff error (GenomicRanges)

2013-09-03 Thread Hervé Pagès
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

Re: [Bioc-devel] 'GRangesList' does not keep metadata of items

2013-09-03 Thread Hervé Pagès
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

Re: [Bioc-devel] 'GRangesList' does not keep metadata of items

2013-09-03 Thread Hervé Pagès
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")