gistfile1.r

setwd('/Users/oho/Desktop/Methylation/')
load('probes.450k.rda')

data <- probes.450k

probes <- data$Probe_ID
length(probes)
bedMatrix <- matrix(nrow=length(probes), ncol=6)

for (i in 1:length(probes)) {
  row <- data[i,]
  coord <- row$coordinate
  strand <- row$strand

  if (strand == '+') {
    start <- coord
    end <- coord + nchar(row$sequence) - 1
    }
  else {
    end <- coord + 1
    start <- coord - nchar(row$sequence) + 2
    }  

  name <- row$Probe_ID
  chrom <- paste('chr', row$chr, sep='')
  
  if (row$Design == 'II') {
    score <- 2
  }
  else {
    score <- 1
  }  

  bedRow <- c(chrom, start, end, name, score, strand)
#  print(paste(bedRow, sep=' '))
  bedMatrix[i, ] <- bedRow
  
}

write.table(bedMatrix, file='450kprobes.bed', quote=F, row.names=F, 
            col.names=F, sep='\t')