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### R code from vignette source 'tRanslatome_package.Rnw'
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### code chunk number 1: tRanslatome_package.Rnw:55-75
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##loading the tRanslatome package
library(tRanslatome)
##loading the training data set
data(tRanslatomeSampleData)
translatome.analysis <- newTranslatomeDataset(expressionMatrix,
c("tot.undiff.a", "tot.undiff.b", "tot.undiff.c"),
c("tot.diff.a", "tot.diff.b", "tot.diff.c"),
c("pol.undiff.a", "pol.undiff.b", "pol.undiff.c"),
c("pol.diff.a", "pol.diff.b", "pol.diff.c"),
label.level= c("transcriptome", "translatome"),
label.condition=c("undifferentiated", "differentiated"))
##identification of DEGs with the use of the limma statistical method
limma.DEGs <- computeDEGs(translatome.analysis,
method= "limma", mult.cor=TRUE)
##enrichment analysis of the selected DEGs
CCEnrichment <- GOEnrichment(limma.DEGs,ontology="CC", classOfDEGs="up",
test.method="elim", test.threshold = 0.05)
##performing a comparison of the biological themes enriched
##in the two levels of gene expression
CCComparison <- GOComparison(CCEnrichment)
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