[Bioc-devel] Change in the coverage function?
Nicolas Delhomme
delhomme at embl.de
Thu Aug 9 12:37:20 CEST 2012
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.
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
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