comparison findBlocks/findBlocks.R @ 0:fea57210de6c draft

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0:fea57210de6c

require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
require("minfi", quietly = TRUE)

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

args <- commandArgs(trailingOnly = TRUE)

input = args[1]
output = args[2]

GRset <- get(load(input))

blocks <- blockFinder(GRset, design, coef = 2, what = c("Beta", "M"),
            cluster = NULL, cutoff = NULL,
            pickCutoff = FALSE, pickCutoffQ = 0.99,
            nullMethod = c("permutation","bootstrap"),
            smooth = TRUE, smoothFunction = locfitByCluster,
            B = ncol(permutations), permutations = NULL,
            verbose = TRUE)

write.table(blocks, output)