Codice Rimasto Pipeline FARGA

#Analisi di espressione genica differenziale - Cellina.Ripe-Salella.Ripe
B.LvsP <- makeContrasts(Cellina.Ripe-Salella.Ripe, levels=design)
res <- glmQLFTest(fit, contrast=B.LvsP)
opt <- getOption("max.print")
options(max.print=1000000000)
sink("topTags_total_Cellina.Ripe-Salella.Ripe.txt")
topTags(res, n=10000000)
sink()
options(max.print=opt)
is.de <- decideTestsDGE(res, adjust.method="BH")
opt <- getOption("max.print")
options(max.print=1000000000)
sink("summary_Cellina.Ripe-Salella.Ripe.txt")
summary(is.de)
sink()
options(max.print=opt)
plotMD(res, status=is.de, values=c(1,-1), col=c("cyan","green"), legend="topright")


#Analisi di espressione genica differenziale - Ruveia.Turn-Salella.Turn
B.LvsP <- makeContrasts(Ruveia.Turn-Salella.Turn, levels=design)
res <- glmQLFTest(fit, contrast=B.LvsP)
opt <- getOption("max.print")
options(max.print=1000000000)
sink("topTags_total_Ruveia.Turn-Salella.Turn.txt")
topTags(res, n=10000000)
sink()
options(max.print=opt)
is.de <- decideTestsDGE(res, adjust.method="BH")
opt <- getOption("max.print")
options(max.print=1000000000)
sink("summary_Ruveia.Turn-Salella.Turn.txt")
summary(is.de)
sink()
options(max.print=opt)
plotMD(res, status=is.de, values=c(1,-1), col=c("cyan","green"), legend="topright")


#Analisi di espressione genica differenziale - Ruveia.Ripe-Salella.Ripe
B.LvsP <- makeContrasts(Ruveia.Ripe-Salella.Ripe, levels=design)
res <- glmQLFTest(fit, contrast=B.LvsP)
opt <- getOption("max.print")
options(max.print=1000000000)
sink("topTags_total_Ruveia.Ripe-Salella.Ripe.txt")
topTags(res, n=10000000)
sink()
options(max.print=opt)
is.de <- decideTestsDGE(res, adjust.method="BH")
opt <- getOption("max.print")
options(max.print=1000000000)
sink("summary_Ruveia.Ripe-Salella.Ripe.txt")
summary(is.de)
sink()
options(max.print=opt)
plotMD(res, status=is.de, values=c(1,-1), col=c("cyan","green"), legend="topright")