[Bioc-devel] Change in the coverage function?

[Nicolas Delhomme]

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