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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
author rnateam
date Wed, 21 Dec 2016 17:30:57 -0500
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
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diff changeset
1 library("methylKit")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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3 file.list = list("input_test1.myCpG.txt", "input_test2.myCpG.txt", "input_control1.myCpG.txt", "input_control2.myCpG.txt")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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5 myobj=methRead( file.list,
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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6 sample.id=list("test 1","test 2","control 1","control 2"),assembly="hg18",pipeline="amp",treatment=c(1,1,0,0))
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
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8 pdf('output_statistics.pdf')
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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9 for (obj in myobj){
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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10 getMethylationStats(obj,plot=TRUE,both.strands=FALSE)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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11 getCoverageStats(obj,plot=TRUE,both.strands=FALSE)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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12 }
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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13 devname = dev.off()
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
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15 # unite function
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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16 methidh = unite(myobj)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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18 pdf("output_correlation.pdf")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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19 getCorrelation(object = methidh, plot=TRUE, method = "pearson")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
rnateam
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20 devname = dev.off()
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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22 # differential methylation
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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23 myDiff = calculateDiffMeth(methidh, overdispersion="none",
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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24 adjust="SLIM", effect="wmean", test="Chisq",
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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25 slim=FALSE, weighted.mean=FALSE)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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27 bedgraph(myDiff, file.name="output_myDiff.bedgraph", col.name="meth.diff",
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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28 unmeth=FALSE, log.transform=FALSE, negative=FALSE, add.on="")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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30 MethPerChr = diffMethPerChr(myDiff, plot=FALSE,
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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31 qvalue.cutoff=0.01,
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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32 meth.cutoff=25)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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33 write.table(MethPerChr, sep="\t", row.names=FALSE, quote=FALSE, file="output_MethPerChr.tsv")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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35 MethylDiff = getMethylDiff(myDiff, difference=25,
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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36 qvalue=0.01, type="all")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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37 bedgraph(MethylDiff, file.name="output_MethylDiff.bedgraph", col.name="meth.diff",
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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38 unmeth=FALSE,log.transform=FALSE,negative=FALSE,add.on="")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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40 pdf( "output_clustering.pdf" )
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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41 methClust = clusterSamples(methidh, dist="correlation", method="ward")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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42 devname = dev.off()
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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44 pdf( "output_PCA.pdf" )
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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45 PCASamples(methidh)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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46 devname = dev.off()
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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48 ## methSeg works for methylRaw or methylDiff with resolution region,
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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49 ## so methylBase has to be tiled before
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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50 tileRaw = tileMethylCounts(myobj[[1]])
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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51 tileBase = tileMethylCounts(methidh)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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52 tileDiff = calculateDiffMeth(tileBase)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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54 ## methseg generates Granges
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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55 segRaw = methSeg(tileRaw, diagnostic.plot = FALSE)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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56 segDiff = methSeg(tileDiff, diagnostic.plot = FALSE)
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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58 ## and can be exported as BED
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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59 methSeg2bed(segments = segRaw, filename = "output_seg_raw.bed")
a8705df7c57f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b
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60 methSeg2bed(segments = segDiff, filename = "output_seg_diff.bed")