[Bioc-sig-seq] strand problem in GenomicRanges

[Hervé Pagès]

Hi Joseph,

I cannot reproduce this (but I'm still using R-2.12.0):

 > library(GenomicRanges)
 > 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) <- "*"
 >
 > z
GRanges with 3 ranges and 0 elementMetadata values
     seqnames     ranges strand |
        <Rle>  <IRanges>  <Rle> |
[1]     chr1 [  1,  50]      * |
[2]     chr2 [300, 349]      * |
[3]     chr3 [600, 649]      * |

seqlengths
  chr1 chr2 chr3
    NA   NA   NA
 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
  [7] LC_PAPER=en_US.utf8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 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

What's puzzling me is all those packages loaded via a namespace
that you get. Could it be that something went wrong with your update
from R-2.12.0 to R-2.12.1? I would suggest you reinstall IRanges and
GenomicRanges from scratch see if that solves the problem (and if
it does, then I would suggest you reinstall all your packages from
scratch).

Cheers,
H.

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
>
>> 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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