[Bioc-sig-seq] strand problem in GenomicRanges

[Joseph Scandura]

Thanks Martin/Hervé: 

I started with a fresh R instance and the problem went away.  I reloaded my old workspace and everything works there as well so I'm not sure what was causing the trouble but now that it is gone, I'm much less interested in figuring it out. Thanks for your help. 

Joe

On Jan 18, 2011, at 3:58 PM, Martin Morgan wrote:

> On 01/17/2011 04:05 PM, Joseph Scandura wrote:
>> I recently updated BioC to 2.12.1 and now find a new issue when assigning strand to a GRanges object. 
>> 
>> The problem must be something straightforward but I have not been able to track it down. 
>> 
>> ################### Example: 
>>> z=GRanges(seqnames=paste("chr",seq(3), sep=""), ranges = IRanges(start=c(1,300,600), width=50), strand=c("+", "-", "*"))
>>> strand(z)
>> 	'factor' Rle of length 3 with 3 runs
>> 	  Lengths: 1 1 1
>> 	  Values : + - *
>> 	Levels(3): + - *
>>> strand(z) = "*"  #this used to assign a strand of "*" to all elements in z
>> Error in x[[name, exact = FALSE]] : 
>>  missing '[[' method for Sequence class GRanges
> 
> Hi Joe -- I don't see this in a new R session; I think what happens is
> that the wrong 'update' is being called, e.g., stats::update rather than
> GRanges::update. Not really sure what to suggest, other than debugging
> by figuring out which of the loaded packages is causing problems. This
> could be tedious.
> 
> Other possibilities are to start R with the --vanilla argument (so that
> no .RData files are loaded on start-up) and to explicitly
> 
>  library(GenomicRanges)
> 
> at the start of your session.
> 
> Here's what I see...
> 
>> library(GenomicRanges)
> Loading required package: IRanges
> 
> Attaching package: 'IRanges'
> 
> The following object(s) are masked from 'package:base':
> 
>    cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin,
>    pmin.int, rbind, rep.int, table
> 
>> z=GRanges(seqnames=paste("chr",seq(3), sep=""), ranges =
> + IRanges(start=c(1,300,600), width=50), strand=c("+", "-", "*"))
>> strand(z)
> 'factor' Rle of length 3 with 3 runs
>  Lengths: 1 1 1
>  Values : + - *
> Levels(3): + - *
>> strand(z) = "*"
>> sessionInfo()
> R version 2.12.0 Patched (2010-11-21 r53647)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] GenomicRanges_1.2.3 IRanges_1.8.8
> 
> Martin
> 
>> 
>>> traceback()
>> 10: stop("missing '[[' method for Sequence class ", class(x))
>> 9: x[[name, exact = FALSE]]
>> 8: x[[name, exact = FALSE]]
>> 7: object$call
>> 6: object$call
>> 5: update.default(x, strand = value)
>> 4: update(x, strand = value)
>> 3: update(x, strand = value)
>> 2: `strand<-`(`*tmp*`, value = "*")
>> 1: `strand<-`(`*tmp*`, value = "*")
>> 
>>> sessionInfo()
>> R version 2.12.1 (2010-12-16)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats   utils   methods base   
>> 
>> other attached packages:
>> [1] GenomicRanges_1.2.3 IRanges_1.8.8       Biobase_2.10.0     
>> 
>> loaded via a namespace (and not attached):
>> [1] annotate_1.28.0                     AnnotationDbi_1.12.0                biomaRt_2.6.0                      
>> [4] Biostrings_2.18.2                   BSgenome_1.18.2                     BSgenome.Ecoli.NCBI.20080805_1.3.16
>> [7] ChIPpeakAnno_1.6.0                  DBI_0.2-5                           DESeq_1.2.1                        
>> [10] gdata_2.8.1                         genefilter_1.32.0                   geneplotter_1.28.0                 
>> [13] GO.db_2.4.5                         gplots_2.8.0                        graphics_2.12.1                    
>> [16] grDevices_2.12.1                    grid_2.12.1                         gtools_2.6.2                       
>> [19] limma_3.6.9                         MASS_7.3-9                          multtest_2.6.0                     
>> [22] org.Hs.eg.db_2.4.6                  RColorBrewer_1.0-2                  RCurl_1.5-0                        
>> [25] RMySQL_0.7-5                        RSQLite_0.9-4                       splines_2.12.1                     
>> [28] survival_2.36-2                     tools_2.12.1                        XML_3.2-0                          
>> [31] xtable_1.5-6       
>> ###################
>> Joe
>> 
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> 
> 
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