Mercurial > repos > kpbioteam > chipseeker_test2

annotate ChIPseeker_test2.R @ 1:43bd1a949ee2 draft default tip

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planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
author kpbioteam
date Mon, 09 Apr 2018 07:11:40 -0400
parents c1eac77337ae
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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1 require(ChIPseeker,quiet=TRUE)
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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2 require(TxDb.Mmusculus.UCSC.mm9.knownGene,quiet=TRUE)
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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3 require(org.Mm.eg.db,quiet=TRUE)
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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5 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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7 # we need that to not crash galaxy with an UTF8 error on German LC settings.
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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10 args <- commandArgs(trailingOnly = TRUE)
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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12 input = args[1]
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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13 output1 = args[2]
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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14 output2 = args[3]
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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16 #output4 = args[5]
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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18 txdb<- TxDb.Mmusculus.UCSC.mm9.knownGene
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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20 peakAnno <- annotatePeak(input, tssRegion=c(-5000, 5000),
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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21 TxDb=txdb, annoDb="org.Mm.eg.db")
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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25 write.table(as.data.frame(peakAnno),file=output1,row.names=FALSE,sep="\t")
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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27 pdf(file=output2)
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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28 plotAnnoPie(peakAnno)
c1eac77337ae planemo upload for repository https://github.com/kpbioteam/ChIPseeker_test2
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29 dev.off()
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