comparison findDMR/findDMR.R @ 6:a0e3f4efb03f draft

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5:715d03e1fd83

require("minfi", quietly = TRUE)
require("ChIPseeker", quietly = TRUE)
require("ChIPpeakAnno", quietly = TRUE)
require("data.table", quietly = TRUE)


args <- commandArgs(trailingOnly = TRUE)
GSMTable = args[1]
platform = args[2]
Data_Table = args[3]
cutoff = as.numeric(args[4])
clusterSize = as.numeric(args[5])
DMR = args[6]

TAB = fread(GSMTable)

IlmnInfo = fread(platform)

gmSet = fread(Data_Table)

# bumphunter Run with processed data
designMatrix <- model.matrix( ~ TAB$Phenotype)

bumps <- bumphunter(
  as.matrix(gmSet),
  design = designMatrix,
  pos = IlmnInfo$BP,
  cutoff = cutoff,
  chr = IlmnInfo$CHR
)

# choose DMR's of a certain length threshold
DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ]
DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end)



write.table(
  DMRInfo,
  DMR,
  quote = F,
  sep = "\t",
  row.names = F,
  col.names = F
)

6:a0e3f4efb03f

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)