Hi,

I have a small RRBS methylation dataset comprising of about 10000 CpG positions (rows) and 10 subjects (columns). I would like make a graph that shows the mean methylation of the CpG around the TSS, i.e. mean methylation on the Y-axis, and distance from TSS on the X-axis. I also have a file, downloaded from UCSC, that shows the TSS start sites for each gene.

I am trying to use the Repitools & GenomiRanges packages to help me do this. The user manual indicates that I need to Some sample code:

##----------------------------
probes <- data.frame(position=seq(1000, 3000, by = 200), chr = "chrX", strand = '-')
genes <- data.frame(chr = "chrX", start=c(2100, 1000), end = c(3000, 2200),
                    strand=c("+","-"))
rownames(genes) <- paste("gene", 1:2, sep = '')

r5 <- annotationLookup(probes, genes, 500, 500)

tmat <- matrix(rnorm(253),11,23)
ids <- paste(probes[,'chr'],probes[,'position'],sep='_')
rownames(tmat) <- ids
colnames(tmat) <- paste('s',1:ncol(tmat),sep='')


##-------------------------

The user manual for Repitools indicates that I should be using the significancePlots function - but there is no method of that name listed (when I do "> ls("package:Repitools").

How should I go about using the sample data above to make my graph? Is Repitools the best (in my case, the simplest) package that I can use?

Any help would be highly appreciated!

thanks!

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