### R code from vignette source 'tRanslatome_package.Rnw' ### Encoding: UTF-8 ################################################### ### code chunk number 1: tRanslatome_package.Rnw:55-75 ################################################### ##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)