[Bioc-devel] as.table not available for HitsList anymore?

[Nicolas Delhomme]

Hej Hervé (I guess that ones for you :-)!

In R dev / Bioc 3.3; calling as.table on an HitsList stopped working:

Browse[2]> ovl
HitsList of length 6
names(6): chr2L chr2R chr3L chr3R chr4 chrX
Browse[2]> as.table(ovl)
Error during wrapup: cannot coerce to a table

I suppose this may have to do with the refactoring of the IRanges/S4Vectors packages? Will the functionality be re-instated, or should I switch my code to using as.matrix instead?

My session info:

R Under development (unstable) (2015-12-15 r69777)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RnaSeqTutorial_0.9.0 easyRNASeq_2.7.2    

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2          futile.logger_1.4.1        
 [3] GenomeInfoDb_1.7.3          XVector_0.11.1             
 [5] futile.options_1.0.0        bitops_1.0-6               
 [7] tools_3.3.0                 zlibbioc_1.17.0            
 [9] biomaRt_2.27.2              annotate_1.49.0            
[11] RSQLite_1.0.0               lattice_0.20-33            
[13] DBI_0.3.1                   parallel_3.3.0             
[15] DESeq_1.23.0                genefilter_1.53.0          
[17] hwriter_1.3.2               Biostrings_2.39.3          
[19] S4Vectors_0.9.15            IRanges_2.5.18             
[21] locfit_1.5-9.1              stats4_3.3.0               
[23] grid_3.3.0                  LSD_3.0                    
[25] Biobase_2.31.3              AnnotationDbi_1.33.3       
[27] XML_3.98-1.3                survival_2.38-3            
[29] BiocParallel_1.5.1          limma_3.27.6               
[31] latticeExtra_0.6-26         geneplotter_1.49.0         
[33] lambda.r_1.1.7              edgeR_3.13.4               
[35] intervals_0.15.1            Rsamtools_1.23.1           
[37] genomeIntervals_1.27.0      splines_3.3.0              
[39] BiocGenerics_0.17.2         GenomicAlignments_1.7.3    
[41] GenomicRanges_1.23.7        ShortRead_1.29.1           
[43] SummarizedExperiment_1.1.11 xtable_1.8-0               
[45] RCurl_1.95-4.7 

Thanks!

Nico

PS Have a good Christmas time!

---------------------------------------------------------------
Nicolas Delhomme, PhD

Acting Manager
UPSC bioinformatics core facility
Umeå Plant Science Center,
Swedish University for Agricultural 
Sciences (SLU) and Umeå University

Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------