Mercurial > repos > kpbioteam > minfi_ppquantile
comparison minfi_ppquantile.R @ 0:41ab8ba3a901 draft default tip
planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
| author | kpbioteam |
|---|---|
| date | Sun, 11 Feb 2018 07:35:45 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:41ab8ba3a901 |
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| 1 require("minfi", quietly = TRUE) | |
| 2 | |
| 3 args <- commandArgs(trailingOnly = TRUE) | |
| 4 | |
| 5 input = args[1] | |
| 6 output = args[2] | |
| 7 | |
| 8 RGSet <- get(load(input)) | |
| 9 | |
| 10 GRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE, | |
| 11 removeBadSamples = TRUE, badSampleCutoff = 10.5, | |
| 12 quantileNormalize = TRUE, stratified = TRUE, | |
| 13 mergeManifest = FALSE, sex = NULL) | |
| 14 | |
| 15 save(GRSet,file = output) |