[BioC] no 'strands' method on GenomicData in 2.5?

Paul Shannon pshannon at systemsbiology.org
Mon Aug 3 17:38:28 CEST 2009


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?


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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