[Bioc-sig-seq] strand problem in GenomicRanges
Martin Morgan
mtmorgan at fhcrc.org
Tue Jan 18 21:58:09 CET 2011
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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