Hello!! 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) locale: [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 [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 -- Sent via the guest posting facility at bioconductor.org.

Hi Joel, You can find the coordinates of the predicted loci in the '@coordinates' slot of the lociData object that is produced by classifySeg or heuristicSeg. If you have used the 'getLikes = TRUE' option in the classifySeg or heuristicSeg functions, or applied the lociLikelihoods function, you may want to use the '@loclikelihoods' slot to filter these coordinates - I usually use something along the lines of: classSegs at coordinates[rowSums(classSegs at loclikelihoods > log(0.9)) > 0] to get the coordinates of all loci with a likelihood greater than 90% in some replicate group, but your needs may vary. Best wishes, Tom On 21/01/14 16:47, Joel RodrXXguez-Medina [guest] wrote: > Hello!! > > 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) > > locale: > [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 > [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 > > -- > Sent via the guest posting facility at bioconductor.org. -- Dr. Thomas J. Hardcastle Department of Plant Sciences University of Cambridge Downing Street Cambridge, CB2 3EA United Kingdom