## ---- message=F, warning=F---------------------------------------------------- library("SISPA") load("data.rda") ExpressionSet[1:5,1:5] ## ---- message=F, warning=F, fig.width = 6, fig.height = 4.5, fig.cap="Identified changepoints on the underlying data zscores"---- sampleScores <- SISPA(feature=1,f1.df=ExpressionSet,f1.profile="up") head(sampleScores) ## ---- message=F, warning=F, fig.width = 4.5, fig.height = 3, fig.cap="Waterfall plot of zscores for samples with (orange) and without profile activity (grey)"---- waterfallplot(sampleScores) ## ---- message=F, warning=F, fig.width = 4.5, fig.height = 3, fig.cap="Bar plot distribution of samples with (orange) and without profile activity"---- freqplot(sampleScores) ## ---- message=F, warning=F, fig.width = 6, fig.height = 4.5, fig.cap="Identified changepoints on the underlying data zscores"---- sampleScores <- SISPA(feature=2,f1.df=ExpressionSet,f1.profile="up", f2.df=VariantSet,f2.profile="up") head(sampleScores) ## ---- message=F, warning=F, fig.width = 4.5, fig.height = 3, fig.cap="Waterfall plot of zscores for samples with (orange) and without profile activity (grey)"---- waterfallplot(sampleScores) ## ---- message=F, warning=F, fig.width = 4.5, fig.height = 3, fig.cap="Bar plot distribution of samples with (orange) and without profile activity"---- freqplot(sampleScores)