Mercurial > repos > biotechcoder > riboseqr_wrapper
comparison test-data/reference.R @ 0:e01de823e919 draft default tip
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| author | biotechcoder |
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| date | Fri, 01 May 2015 05:41:51 -0400 |
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| -1:000000000000 | 0:e01de823e919 |
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| 1 library(riboSeqR) | |
| 2 fastaCDS_REF <- findCDS(fastaFile='rsem_chlamy236_deNovo.transcripts.fa', startCodon=c("ATG"), stopCodon=c("TAG", "TAA", "TGA")) | |
| 3 ribofiles <- paste("chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "") | |
| 4 rnafiles <- paste("chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "") | |
| 5 riboDat_REF <- readRibodata(ribofiles, rnafiles, replicates=c("WT", "WT", "M", "M")) | |
| 6 fCs_REF <- frameCounting(riboDat_REF, fastaCDS_REF) | |
| 7 fS_REF <- readingFrame(rC = fCs_REF) | |
| 8 | |
| 9 pdf(file="/tmp/Periodicity-plot.pdf") | |
| 10 plotFS(fS_REF, legend.text = c('Frame 0', 'Frame 1', 'Frame 2')) | |
| 11 dev.off() | |
| 12 | |
| 13 ffCs_REF <- filterHits(fCs_REF, lengths=c(27,28), frames=list(1,0), hitMean = 50, unqhitMean = 10, fS=fS_REF) | |
| 14 pdf(file='/tmp/Metagene-analysis-plot.pdf') | |
| 15 plotCDS(coordinates=ffCs_REF@CDS, riboDat=riboDat_REF, lengths=27) | |
| 16 plotCDS(coordinates=ffCs_REF@CDS, riboDat=riboDat_REF, lengths=28) | |
| 17 dev.off() | |
| 18 | |
| 19 pdf(file='/tmp/Ribosome-profile-plot.pdf') | |
| 20 plotTranscript("CUFF.37930.1", coordinates=ffCs_REF@CDS, riboData=riboDat_REF, length=27, cap=200) | |
| 21 dev.off() | |
| 22 | |
| 23 riboCounts_REF <- sliceCounts(ffCs_REF, lengths = c(27,28), frames = list(0,2)) | |
| 24 rnaCounts_REF <- rnaCounts(riboDat_REF, ffCs_REF@CDS) | |
| 25 | |
| 26 save('fastaCDS_REF', 'riboDat_REF', 'fCs_REF', 'fS_REF', 'ffCs_REF', 'riboCounts_REF', 'rnaCounts_REF', file='Robjects.rda') | |
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