[BioC] Get actual coordinates for the predicted loci

Tom Hardcastle tjh48 at cam.ac.uk
Wed Jan 22 10:58:47 CET 2014

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,


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
> 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

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