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al2na/methSegDemo.R

Last active August 29, 2015 14:23
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methseg usage and installation
Raw
methSegDemo.R
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")
Raw
methSegInstall.R
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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