no 'strands' method on GenomicData in 2.5?
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Paul Shannon ★ 1.1k
@paul-shannon-578
Last seen 7.9 years ago
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
hgu133plus2 rtracklayer IRanges hgu133plus2 rtracklayer IRanges • 596 views
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@michael-lawrence-2759
Last seen 7.9 years ago
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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