comparison findDMR/findDMR.R @ 12:083895dbc289 draft

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11:24ac6f93cc3e

require("BiocGenerics", quietly = TRUE)
require("data.table", quietly = TRUE)
require("bumphunter", 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
)

12:083895dbc289

require("minfi", quietly = TRUE)

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

args <- commandArgs(trailingOnly = TRUE)
input1 = args[1]
input2 = args[2]
cutoff = as.numeric(args[3])
B = as.numeric(args[4]) 
pickCutoffQ = as.numeric(args[5])
output1 = args[6]
output2 = args[7]

GRset <- get(load(input1))

pheno <- fread(input2)

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

dmrs <- bumphunter(GRset, design = designMatrix,
                   cutoff =cutoff, B=B, type="Beta",  pickCutoff=TRUE,
                   pickCutoffQ=pickCutoffQ)

DMRTable <- dmrs$table

write.table(DMRTable, output1)

sign=sign(DMRTable$value)

sign[sign==-1]="-"
sign[sign==1]="+"

dmr_track<-cbind(as.character(DMRTable$chr),DMRTable$start,DMRTable$end,sign)

write.table(dmr_track,output2,quote = FALSE, sep = "\t\t\t\t",row.names = FALSE, col.names = FALSE,append=TRUE)