[BioC] Get actual coordinates for the predicted loci
tjh48 at cam.ac.uk
Wed Jan 22 10:58:47 CET 2014
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.
On 21/01/14 16:47, Joel RodrXXguez-Medina [guest] wrote:
> 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():
> 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
> Sent via the guest posting facility at bioconductor.org.
Dr. Thomas J. Hardcastle
Department of Plant Sciences
University of Cambridge
Cambridge, CB2 3EA
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