Mercurial > repos > kpbioteam > minfi_ppquantile

diff minfi_ppquantile.R @ 0:41ab8ba3a901 draft default tip

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planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
author kpbioteam
date Sun, 11 Feb 2018 07:35:45 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppquantile.R	Sun Feb 11 07:35:45 2018 -0500
@@ -0,0 +1,15 @@
+require("minfi", quietly = TRUE)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input = args[1]
+output = args[2]
+
+RGSet <- get(load(input))
+
+GRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE,
+  removeBadSamples = TRUE, badSampleCutoff = 10.5,
+  quantileNormalize = TRUE, stratified = TRUE, 
+  mergeManifest = FALSE, sex = NULL)
+
+save(GRSet,file = output)