[BioC] Get actual coordinates for the predicted loci
Joel RodrÃguez-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?
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 segmentSeq_1.14.0 ShortRead_1.20.0 Rsamtools_1.14.2 lattice_0.20-24 Biostrings_2.30.1
 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):
 Biobase_2.22.0 bitops_1.0-6 grid_3.0.2 hwriter_1.3 latticeExtra_0.6-26 RColorBrewer_1.0-5
 stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0
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