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1 library(riboSeqR)
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2 fastaCDS_REF <- findCDS(fastaFile='rsem_chlamy236_deNovo.transcripts.fa', startCodon=c("ATG"), stopCodon=c("TAG", "TAA", "TGA"))
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3 ribofiles <- paste("chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
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4 rnafiles <- paste("chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")
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5 riboDat_REF <- readRibodata(ribofiles, rnafiles, replicates=c("WT", "WT", "M", "M"))
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6 fCs_REF <- frameCounting(riboDat_REF, fastaCDS_REF)
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7 fS_REF <- readingFrame(rC = fCs_REF)
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8
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9 pdf(file="/tmp/Periodicity-plot.pdf")
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10 plotFS(fS_REF, legend.text = c('Frame 0', 'Frame 1', 'Frame 2'))
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11 dev.off()
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12
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13 ffCs_REF <- filterHits(fCs_REF, lengths=c(27,28), frames=list(1,0), hitMean = 50, unqhitMean = 10, fS=fS_REF)
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14 pdf(file='/tmp/Metagene-analysis-plot.pdf')
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15 plotCDS(coordinates=ffCs_REF@CDS, riboDat=riboDat_REF, lengths=27)
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16 plotCDS(coordinates=ffCs_REF@CDS, riboDat=riboDat_REF, lengths=28)
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17 dev.off()
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18
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19 pdf(file='/tmp/Ribosome-profile-plot.pdf')
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20 plotTranscript("CUFF.37930.1", coordinates=ffCs_REF@CDS, riboData=riboDat_REF, length=27, cap=200)
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21 dev.off()
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22
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23 riboCounts_REF <- sliceCounts(ffCs_REF, lengths = c(27,28), frames = list(0,2))
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24 rnaCounts_REF <- rnaCounts(riboDat_REF, ffCs_REF@CDS)
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25
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26 save('fastaCDS_REF', 'riboDat_REF', 'fCs_REF', 'fS_REF', 'ffCs_REF', 'riboCounts_REF', 'rnaCounts_REF', file='Robjects.rda')
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