GenomeGraphs 1.4.0 fails to plot empty GeneRegion
0
0
Entering edit mode
Tim Rayner ▴ 270
@tim-rayner-2913
Last seen 10.2 years ago
Hi, I don't know if this is by accident or design, but some code I had working with GenomeGraphs 1.2.3 is now failing under version 1.4.0. I've reduced the problem to the following test case: > require('biomaRt') > require('GenomeGraphs') > mart <- useDataset('hsapiens_gene_ensembl', useMart('ensembl')) > genesminus <- makeGeneRegion(start = 10662805, end = 10718158, strand = "-", chromosome=12, biomart=mart) > genesplus <- makeGeneRegion(start = 10662805, end = 10718158, strand = "+", chromosome=12, biomart=mart) > gdPlot(list('minus strand'=genesminus, 'plus strand'=genesplus)) This draws the minus strand just fine, but the plus strand (which, I think crucially, retrieves no genes) fails with the following message: "Error in if (ens[1, 6] == 1) { : missing value where TRUE/FALSE needed" I know that the same code running under R 2.8.1/BioC 2.3/GenomeGraphs 1.2.3 draws both strands without complaining. Is this change to GenomeGraphs behaviour intentional, or can this be considered a bug? Many thanks, Tim > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-apple-darwin9.6.0 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomeGraphs_1.4.0 biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.94-1 XML_2.3-0
GenomeGraphs GenomeGraphs • 974 views
ADD COMMENT

Login before adding your answer.

Traffic: 739 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6