[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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