Mercurial > repos > kpbioteam > minfi_ppquantile
changeset 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 | |
| files | RGSet.rdata minfi_ppquantile.R minfi_ppquantile.xml quantile.rdata test-data/RGSet.rdata test-data/quantile.rdata |
| diffstat | 6 files changed, 44 insertions(+), 0 deletions(-) [+] |
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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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_ppquantile.xml Sun Feb 11 07:35:45 2018 -0500 @@ -0,0 +1,29 @@ +<tool id="minfi_ppquantile" name="minfi_ppquantile" version="0.1.0"> + <description>implements stratified quantile normalization preprocessing</description> + <requirements> + <requirement type="package" version="1.24.0">bioconductor-minfi</requirement> + <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement> + <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript ${__tool_directory__}/minfi_ppquantile.R "$input1" "$output1" + ]]></command> + <inputs> + <param type="data" name="input1" format="rdata" /> + </inputs> + <outputs> + <data name="output1" format="rdata" /> + </outputs> + <tests> + <test> + <param name="input1" value="RGSet.rdata"/> + <output name="output1" file="quantile.rdata"/> + </test> + </tests> + <help><![CDATA[ + The normalization procedure is applied to the Meth and Unmeth intensities separately. The distribution of type I and type II signals is forced to be the same by first quantile normalizing the type II probes across samples and then interpolating a reference distribution to which we normalize the type I probes. Since probe types and probe regions are confounded and we know that DNAm distributions vary across regions we stratify the probes by region before applying this interpolation. + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu049</citation> + </citations> +</tool> \ No newline at end of file