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
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
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