|
0
|
1 require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
|
|
|
2 require("minfi", quietly = TRUE)
|
|
|
3
|
|
|
4 options(warn = -1)
|
|
|
5 options("download.file.method"="wget")
|
|
|
6
|
|
|
7 args <- commandArgs(trailingOnly = TRUE)
|
|
|
8
|
|
|
9 input = args[1]
|
|
|
10 output = args[2]
|
|
|
11
|
|
|
12 GRset <- get(load(input))
|
|
|
13
|
|
|
14 blocks <- blockFinder(GRset, design, coef = 2, what = c("Beta", "M"),
|
|
|
15 cluster = NULL, cutoff = NULL,
|
|
|
16 pickCutoff = FALSE, pickCutoffQ = 0.99,
|
|
|
17 nullMethod = c("permutation","bootstrap"),
|
|
|
18 smooth = TRUE, smoothFunction = locfitByCluster,
|
|
|
19 B = ncol(permutations), permutations = NULL,
|
|
|
20 verbose = TRUE)
|
|
|
21
|
|
|
22 write.table(blocks, output)
|
