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methseg usage and installation
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| download.file("https://dl.dropboxusercontent.com/u/1373164/H1.chr21.chr22.rds",destfile="H1.chr21.chr22.rds",method="curl") | |
| mbw=readRDS("H1.chr21.chr22.rds") | |
| # it finds the optimal number of componets as 6 | |
| res=methSeg(mbw,diagnostic.plot=TRUE,maxInt=100,minSeg=10) | |
| # however the BIC stabilizes after 4, we can also try 4 componets | |
| res=methSeg(mbw,diagnostic.plot=TRUE,maxInt=100,minSeg=10,G=1:4) | |
| # get segments to BED file | |
| methSeg2bed(res,filename="H1.chr21.chr22.trial.seg.bed") |
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| install.packages( c("data.table","devtools")) | |
| source("http://bioconductor.org/biocLite.R") | |
| biocLite(c("fastseg","rtracklayer")) | |
| # install the package from github | |
| library(devtools) | |
| install_github("al2na/methylKit",ref="methSeg",build_vignettes=FALSE) |
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