Mercurial > repos > kpbioteam > minfi_ppquantile

annotate 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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41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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diff changeset
1 require("minfi", quietly = TRUE)
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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3 args <- commandArgs(trailingOnly = TRUE)
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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diff changeset
5 input = args[1]
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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6 output = args[2]
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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8 RGSet <- get(load(input))
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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10 GRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE,
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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11 removeBadSamples = TRUE, badSampleCutoff = 10.5,
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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12 quantileNormalize = TRUE, stratified = TRUE,
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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diff changeset
13 mergeManifest = FALSE, sex = NULL)
41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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41ab8ba3a901 planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty
kpbioteam
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15 save(GRSet,file = output)