Mercurial > repos > kpbioteam > chipeakanno_annopeaks

annotate chipeakanno_annopeaks.R @ 4:b5bc7e70b949 draft

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planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit e4ccaafda5f770219ab999f48574a3bfed84c311
author kpbioteam
date Tue, 12 Jun 2018 08:46:36 -0400
parents 9ec5e9e2e7b2
children 17b814d78ac6
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9ec5e9e2e7b2 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit c53721636b1df8f6d7791eb67c86df36e9d97784
kpbioteam
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1 source("https://bioconductor.org/biocLite.R")
9ec5e9e2e7b2 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit c53721636b1df8f6d7791eb67c86df36e9d97784
kpbioteam
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2 biocLite("ChIPpeakAnno")
9ec5e9e2e7b2 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit c53721636b1df8f6d7791eb67c86df36e9d97784
kpbioteam
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9ec5e9e2e7b2 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit c53721636b1df8f6d7791eb67c86df36e9d97784
kpbioteam
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4 biocLite("rtracklayer")
9ec5e9e2e7b2 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit c53721636b1df8f6d7791eb67c86df36e9d97784
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efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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6 require("ChIPpeakAnno", quietly = TRUE)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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7 require("EnsDb.Hsapiens.v75", quietly = TRUE)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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8 require("rtracklayer", quietly = TRUE)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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10 options(warn = -1)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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11 options("download.file.method"="wget")
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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13 args <- commandArgs(trailingOnly = TRUE)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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15 input1 = args[1]
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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16 input2 = args[2]
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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17 input3 = as.numeric(args[3])
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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18 input4 = as.numeric(args[4])
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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19 output1 = args[5]
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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a90b6d85463c planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b7298370ebae64340e792262c4e4f35568757871-dirty
kpbioteam
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21 DMRInfo <- read.table(input1)
a90b6d85463c planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b7298370ebae64340e792262c4e4f35568757871-dirty
kpbioteam
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22 peaks <- GRanges(seqnames = DMRInfo[, 1],
a90b6d85463c planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b7298370ebae64340e792262c4e4f35568757871-dirty
kpbioteam
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23 ranges = IRanges
a90b6d85463c planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b7298370ebae64340e792262c4e4f35568757871-dirty
kpbioteam
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24 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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26 annoData <- toGRanges(EnsDb.Hsapiens.v75)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
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27 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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29 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c(input2), bindingRegion=c(input3, input4))
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
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b5bc7e70b949 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit e4ccaafda5f770219ab999f48574a3bfed84c311
kpbioteam
parents: 3
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31 write.table(anno, file= output1, quote = FALSE, row.names = FALSE, sep = "\t")