inst/doc/SISPA.R

In SISPA: SISPA: Method for Sample Integrated Set Profile Analysis

## ---- 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)