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view findDMR/findDMR.R @ 6:a0e3f4efb03f draft

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author testtool
date Tue, 25 Apr 2017 13:19:29 -0400
parents 715d03e1fd83
children bae8d90853b7
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require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
require("minfi", quietly = TRUE)

options(warn = -1)
options("download.file.method"="wget")

args <- commandArgs(trailingOnly = TRUE)

input1 = args[1]
input2 = args[2]
output = args[3]

GRset <- get(load(input1))

pheno <- fread(input2)

designMatrix <- model.matrix(~ pheno$Phenotype)

dmrs <- bumphunter(GRset, design = designMatrix,
                   cutoff = 0.2, B=0, type="Beta")
write.table(dmrs, output)