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findDMP/._.DS_Store findDMP/findDMP.R findDMP/findDMP.xml findDMP/test-data/._.DS_Store findDMP/test-data/._OLDvsYOUNG.csv findDMP/test-data/DMP.txt findDMP/test-data/OLDvsYOUNG.csv findDMP/test-data/out.RData |
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| diff -r 000000000000 -r 8cf72c018b42 findDMP/findDMP.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMP/findDMP.R Sun Jun 11 17:29:26 2017 -0400 |
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| @@ -0,0 +1,23 @@ +require("minfi", quietly = TRUE) +require("data.table", quietly = TRUE) + +options(warn = -1) +options("download.file.method"="wget") + +args <- commandArgs(trailingOnly = TRUE) + +input1 = args[1] +input2 = args[2] +output = args[3] + +GRset <- get(load(input1)) + +pheno <- read.csv(input2) + +beta <- getBeta(GRset) + +pData <- pData(GRset) + +dmp <- dmpFinder(beta, pheno$Phenotype, type = "continuous") + +write.table(dmp, output) |
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| diff -r 000000000000 -r 8cf72c018b42 findDMP/findDMP.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMP/findDMP.xml Sun Jun 11 17:29:26 2017 -0400 |
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| @@ -0,0 +1,46 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="findDMP" name="findDMP" version="1.20.0"> +<requirements> +<requirement type="package" version="1.20.0">bioconductor-minfi</requirement> +</requirements> +<stdio> +<exit_code range="1:" /> +</stdio> + <command> Rscript $__tool_directory__/findDMP.R "$input1" "$input2" "$output" </command> + <inputs> + <param format="RDdata" name="input1" type="data" label="Genomic Ratio Set" help="e.g. 'GRsetFromGEO tool output'"/> + <param format="csv" name="input2" type="data" label="Phenotype Table" + help="e.g.'ID Phenotype + GSM1255789 OLD + GSM1255798 OLD + GSM1255778 YOUNG'"/> + </inputs> + <outputs> + <data format="text" type="data" name="output" label="DMP.txt"/> + </outputs> + <tests> + <test> + <param name="test"> + <element name="test-data"> + <collection type="data"> + <element name="input1" type="data" format="RData" label="test-data/out.RData"> </element> + <element name="input2" type="data" format="csv" label="test-data/OLDvsYOUNG.csv"> </element> + </collection> + </element> + </param> + <output name="output" type="data" format="text" label="test-data/DMP.txt"/> + </test> + </tests> + <help> +**What it does** +Tool finds differentially methylated positions (DMPs) with respect to a phenotype covariate +**Input** +GenomicRatioSet object +Phenotype Table +**Output** +Text file containing differentially methylated positions + </help> + <citations> +<citation type="doi">10.1093/bioinformatics/btu049</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 8cf72c018b42 findDMP/test-data/DMP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMP/test-data/DMP.txt Sun Jun 11 17:29:26 2017 -0400 |
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| diff -r 000000000000 -r 8cf72c018b42 findDMP/test-data/OLDvsYOUNG.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMP/test-data/OLDvsYOUNG.csv Sun Jun 11 17:29:26 2017 -0400 |
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| @@ -0,0 +1,71 @@ +ID,Phenotype +GSM1255789,OLD +GSM1255798,OLD +GSM1255790,OLD +GSM1255791,OLD +GSM1255792,OLD +GSM1255793,OLD +GSM1255794,OLD +GSM1255795,OLD +GSM1255796,OLD +GSM1255797,OLD +GSM1255827,OLD +GSM1255836,OLD +GSM1255828,OLD +GSM1255829,OLD +GSM1255830,OLD +GSM1255831,OLD +GSM1255832,OLD +GSM1255833,OLD +GSM1255834,OLD +GSM1255835,OLD +GSM1255769,YOUNG +GSM1255778,YOUNG +GSM1255770,YOUNG +GSM1255771,YOUNG +GSM1255772,YOUNG +GSM1255773,YOUNG +GSM1255774,YOUNG +GSM1255775,YOUNG +GSM1255776,YOUNG +GSM1255777,YOUNG +GSM1255809,YOUNG +GSM1255810,YOUNG +GSM1255811,YOUNG +GSM1255812,YOUNG +GSM1255813,YOUNG +GSM1255814,YOUNG +GSM1255815,YOUNG +GSM1255816,YOUNG +GSM1255817,YOUNG +GSM1255789,OLD +GSM1255798,OLD +GSM1255790,OLD +GSM1255791,OLD +GSM1255792,OLD +GSM1255793,OLD +GSM1255794,OLD +GSM1255795,OLD +GSM1255796,OLD +GSM1255797,OLD +GSM1255827,OLD +GSM1255836,OLD +GSM1255828,OLD +GSM1255829,OLD +GSM1255830,OLD +GSM1255831,OLD +GSM1255832,OLD +GSM1255833,OLD +GSM1255834,OLD +GSM1255835,OLD +GSM1255769,YOUNG +GSM1255778,YOUNG +GSM1255770,YOUNG +GSM1255771,YOUNG +GSM1255772,YOUNG +GSM1255773,YOUNG +GSM1255774,YOUNG +GSM1255775,YOUNG +GSM1255776,YOUNG +GSM1255832,OLD +GSM1255833,OLD |
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