Hello Repitools developers,
I am trying to obtain % methylation values from MeDIP samples where I do not have SssI control using BayMeth, but I fail at the first step: the creation of a BayMethList object. This function results in an error if no control is provided. I found no examples of a SssI free analysis in the vignettes nor the supplementary information of the article describing the methods. Can you please provide such an example?
> windows <- genomeBlocks(Hsapiens, chrs="chr21", width=250, spacing=250)
> cpgdens <- cpgDensityCalc(windows, organism=Hsapiens, w.function="linear", window=700)
> sI <- matrix(rnbinom(2*length(windows), mu=5, size=2), ncol=2)
> bm <- BayMethList(windows=windows, sampleInterest=sI, cpgDens=cpgdens)
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘BayMethList’ for signature ‘"GRanges", "missing", "matrix", "numeric"’
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: MarIuX64 2.0 GNU/Linux 2010-2012 locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C  LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C  LC_PAPER=C LC_NAME=C LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  Repitools_1.12.0