[Bioc-devel] Change in the coverage function?

[Hervé Pagès]

Hi Nico,

On 08/09/2012 03:37 AM, Nicolas Delhomme wrote:
> Hi all,
>
> The IRanges coverage function used to return a named RleList when provided with a named IRangesList, which it does not do anymore. It instead returns an unnamed RleList. Has that change been done on purpose? The change occurred relatively recently (in the last week and a half probably) in Bioc 2.11.

Sorry for that. Should be fixed in IRanges 1.15.31.

Cheers,
H.

>
> My sessionInfo()
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.19
>   [2] RnaSeqTutorial_0.0.9
>   [3] easyRNASeq_1.3.9
>   [4] ShortRead_1.15.9
>   [5] latticeExtra_0.6-19
>   [6] RColorBrewer_1.0-5
>   [7] Rsamtools_1.9.25
>   [8] DESeq_1.9.11
>   [9] lattice_0.20-6
> [10] locfit_1.5-8
> [11] BSgenome_1.25.6
> [12] GenomicRanges_1.9.43
> [13] Biostrings_2.25.9
> [14] IRanges_1.15.30
> [15] edgeR_2.99.4
> [16] limma_3.13.16
> [17] biomaRt_2.13.2
> [18] Biobase_2.17.6
> [19] genomeIntervals_1.13.3
> [20] BiocGenerics_0.3.0
> [21] intervals_0.13.3
>
> loaded via a namespace (and not attached):
>   [1] annotate_1.35.3       AnnotationDbi_1.19.28 bitops_1.0-4.1
>   [4] DBI_0.2-5             genefilter_1.39.0     geneplotter_1.35.1
>   [7] grid_2.15.1           hwriter_1.3           RCurl_1.91-1
> [10] RSQLite_0.11.1        splines_2.15.1        stats4_2.15.1
> [13] survival_2.36-14      tools_2.15.1          XML_3.9-4
> [16] xtable_1.7-0          zlibbioc_1.3.0
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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