Can I use trackViewer to generate methylation lolliops with my own gene models and assembly?
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@martinsonjohn-22218
Last seen 21 months ago

I am trying to help someone get some figures generated of some methylation data and she, who has less experience than I with R (which isn't really much) showed me trackViewer and said that the lollipop diagrams she's seen in the examples are exactly what she's is hoping to be able to generate. I started to look at the trackViewer documentation but it isn't clear to me if we can use our own genomic assembly and gene models or if trackViewer is really designed to work primarily (only?) with well established model organisms that have lots of tracks publically available at e.g. UCSC. Before diving in any deeper I thought I'd ask, can I use our own assembly and models (which are in gff3 format), and if so, can you provide or point me to some guidance on how I get those loaded into trackViewer?

Thanks, John Martinson

trackViewer • 160 views
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 17 days ago
United States

Hi John,

You can always generate a TxDb object by functions makeTxDbFromGFF from a local gff file, or makeTxDbFromUCSC, makeTxDbFromBiomart, and makeTxDbFromEnsembl, from online resources in GenomicFeatures package.

For trackViewer to plot lolliplot, you can just input a GRanges object as features and GRanges as the mutation/methylation data. There is no need to have a well defined genome assembly at all. A GRanges object is that object contain the start position, end postition for plot.

Let me know if you still have questions.

Jianhong

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