[BioC] How to run bioHMM on Affymetrix data?

J.Oosting at lumc.nl J.Oosting at lumc.nl
Wed Apr 15 10:37:07 CEST 2009

You will have to create a SegList object in order to do this, for the
runBioHMM() function a SegList needs to have the following components

M.observed: a matrix with the copynumber values samples in columns,
probes in rows
genes: A data.frame with at list a Chr and a Position column

Make sure that the data is already ordered by chromosome and position

# example code starting with vectors of cn.data, chromosome and 
# base.position
observed<- matrix(cn.data[Idx],ncol=1)
segList$M.observed <- observed
segList$genes <-

segList<-new("SegList", segList)


> I am interested in fitting bioHMM on some non-array CGH data using the
> function runBioHMM. Say I have have a vector, y, of processed
> measurements at M SNPs along a chromosome and a vector of
> genomic locations, say pos. How can I use this to run bio HMM?

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