[Bioc-devel] Valid classes for extraColumnSlots

Peter Hickey hickey at wehi.EDU.AU
Tue Aug 26 04:57:15 CEST 2014

Are the extraColumnSlots of a class that extends GenomicRanges limited to DataFrame objects?

Background: I wrote a class that extends the GRanges class. It has a matrix as the extraColumnSlots. When I use replaceROWS,GenomicRanges,GenomicRanges-method (via inheritance) it extracts this extraColumnSlots as a DataFrame object by use of GenomicRanges:::extraColumnSlotsAsDF. This means that the subsequent call to update() in replaceROWS,GenomicRanges,GenomicRanges-method fails because the class definition expects a matrix for the extraSlotNames but gets a DataFrame.

In this case, it's not a problem for me to change my extraColumnSlots element to a DataFrame in the class definition. However, more generally, some guidance on what classes are and are not allowed in extraColumnSlots would be appreciated.


This is using BioC devel:
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
[1] GenomicTuples_0.1.0   GenomicRanges_1.17.35 GenomeInfoDb_1.1.18  
[4] IRanges_1.99.24       S4Vectors_0.1.2       BiocGenerics_0.11.4  
[7] devtools_1.5

loaded via a namespace (and not attached):
 [1] Biobase_2.25.0   digest_0.6.4     evaluate_0.5.5   httr_0.4
 [5] memoise_0.2.1    packrat_0.4.0.12 Rcpp_0.11.2      RCurl_1.95-4.3  
 [9] stats4_3.1.1     stringr_0.6.2    tools_3.1.1      whisker_0.3-2

Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324

hickey at wehi.edu.au

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