Question: SssI free analysis in BayMeth/Repitools
0
gravatar for Matthias Lienhard
4.3 years ago by
Max Planck Institute for molecular Genetics, Berlin, Germany
Matthias Lienhard140 wrote:

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?

Thanks, Matthias

> library("Repitools")
> library(BSgenome.Hsapiens.UCSC.hg19)
> 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:
 [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C           
 [4] LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C       
 [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] Repitools_1.12.0

[...]

repitools • 458 views
ADD COMMENTlink written 4.3 years ago by Matthias Lienhard140
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