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