On Mon, Aug 3, 2009 at 8:38 AM, Paul Shannon <pshannon@systemsbiology.org>wrote:

> While working through the R script that accompanies the 1.5.9 (development)
> version of rtracklayer (and using the development version of IRanges as
> well, 1.3.47), I encountered the error:
>
>    unable to find an inherited method for function "strand", for signature
> "RangedData"
>
> What have I missed?  Is it unwise to mix development versions (in this
> case, of rtracklayer & IRanges) with the release version of other bioc
> packages?
>

In general yes, although in this case I wouldn't expect a problem. What
happens if you type:
showMethods("strand")

Thanks,
Michael


>
>
> Here is the relevant section of the R script.   sessionInfo follows.
>
> head(targets)
> library(IRanges)
> targetRanges <- IRanges(targets$start, targets$end)
> library(rtracklayer)
> targetTrack <- GenomicData(targetRanges,
>                           targets[,c("strand", "name", "target")],
>                           chrom = paste("chr", targets$chrom, sep = ""),
>                           genome = "hg18")
>
>
> ###################################################
> ### chunk number 4: feature-data-accessors
> ###################################################
> head(chrom(targetTrack))
> head(start(targetTrack))
>
>
> ###################################################
> ### chunk number 5: sol-1
> ###################################################
> head(strand(targetTrack))
>
>
>
>
> > sessionInfo ()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.US-ASCII/en_US.US-ASCII/C/C/en_US.US-ASCII/en_US.US-ASCII
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> [7] base
>
> other attached packages:
>  [1] rtracklayer_1.5.9    RCurl_0.94-1         org.Hs.eg.db_2.2.6
>  [4] microRNA_1.2.0       Rlibstree_0.3-1      Biostrings_2.12.1
>  [7] IRanges_1.3.47       limma_2.18.0         genefilter_1.24.0
> [10] humanStemCell_0.2.0  hgu133plus2.db_2.2.5 RSQLite_0.7-1
> [13] DBI_0.2-4            AnnotationDbi_1.6.0  Biobase_2.4.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.22.0 BSgenome_1.12.0 splines_2.9.0   survival_2.35-4
> [5] tools_2.9.0     XML_2.3-0       xtable_1.5-5
>
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