[BioC] Get actual coordinates for the predicted loci

Joel Rodríguez-Medina [guest] guest at bioconductor.org
Tue Jan 21 17:47:15 CET 2014


I recently started using segmentSeq for Illumina sRNA-Seq data, however when doing the examples from the vignette I couldn't find a way to obtain the coordinates for the predicted loci, so to as look them up on a Genome Browser. 

I followed the vignette's examples and the final step is producing a plotGenome object, yet I would like to have access to all the coordinates within the object. Is there a way to achieve this?

Thank you!

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] segmentSeq_1.14.0    ShortRead_1.20.0     Rsamtools_1.14.2     lattice_0.20-24      Biostrings_2.30.1   
 [6] baySeq_1.16.0        GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.6       BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
[1] Biobase_2.22.0      bitops_1.0-6        grid_3.0.2          hwriter_1.3         latticeExtra_0.6-26 RColorBrewer_1.0-5 
[7] stats4_3.0.2        tools_3.0.2         zlibbioc_1.8.0     

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