How to run bioHMM on Affymetrix data?
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@stacey-burrows-2450
Last seen 8.0 years ago
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 intensity measurements at M SNPs along a chromosome and a vector of corresponding genomic locations, say pos. How can I use this to run bio HMM? Thanks for any help, Stacey __________________________________________________________________ [[elided Yahoo spam]] [[alternative HTML version deleted]]
CGH CGH • 585 views
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@oosting-j-path-412
Last seen 8.0 years ago
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 Idx<-order(chromosome,base.position) segList<-list() observed<- matrix(cn.data[Idx],ncol=1) colnames(observed)<-"sample1" segList$M.observed <- observed segList$genes <- data.frame(Chr=chromosome[Idx],Position=base.position[Idx]) segList<-new("SegList", segList) result<-runBioHMM(segList) Jan > 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 intensity > measurements at M SNPs along a chromosome and a vector of corresponding > genomic locations, say pos. How can I use this to run bio HMM? >
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