diff findBlocks/findBlocks.R @ 0:fea57210de6c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findBlocks/findBlocks.R	Sun Jun 11 08:53:04 2017 -0400
@@ -0,0 +1,22 @@
+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)