[BioC] Graph of methylation data around TSS - Repitools or other package?

Dario Strbenac dstr7320 at uni.sydney.edu.au
Thu Nov 21 03:00:15 CET 2013

Hello Tim,

Ensure you are using a current version of Repitools. I checked the manual, and there is no mention of significancePlots. That function was renamed to profilePlots a while ago. Since you want to see all of the sites and are not testing a subset of them, I would use binPlots, and just give all the scores the same ID so they are in the same bin.

The code you use from the example is specific to microarrays. Since you know the coordinates of the CpG islands already, you can provide them as the p.anno argument to featureScores. The first argument is your matrix of values. The anno argument is your annotation of genes from UCSC. Also provide up and down values for how far away from the TSS to plot. Once you have a ScoresList object made by featureScores with this information, you can give that to binPlots.

Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050

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