## ---- message=F, warning=F, eval=F--------------------------------------- # install.packages( c("changepoint", "data.table", "genefilter", "graphics", "HH", "knitr", "latticeExtra", "lattice", "plyr", "scatterplot3d", "stats", "Biobase", "GSEABase") ) ## ---- message=F, warning=F----------------------------------------------- library("GISPA") load("data.rda") exprset varset cnvset ## ---- message=F, warning=F----------------------------------------------- results <- GISPA(feature=2, f.sets=c(exprset,cnvset), g.set=NULL, ref.samp.idx=1, comp.samp.idx=c(2,3), f.profiles=c("up", "up"), cpt.data="var", cpt.method="BinSeg", cpt.max=5) ## ---- message=F, warning=F----------------------------------------------- cptSlopeplot(gispa.output=results,feature=2,type=c("EXP","VAR")) ## ---- message=F, warning=F, fig.width = 7, fig.height = 6---------------- stackedBarplot(gispa.output=results,feature=2,cpt=1,type=c("EXP","CNV"), input.cex=1.5,input.cex.lab=1.5,input.gap=0.5, samp.col=c("red", "green", "blue"), strip.col=c("yellow", "bisque")) ## ---- message=F, warning=F, fig.width = 6, fig.height = 6---------------- propBarplot(gispa.output=results,feature=2,cpt=1,input.cex=0.5,input.cex.lab=0.5,ft.col=c("grey0", "grey60"),strip.col="yellow") ## ---- message=F, warning=F----------------------------------------------- results <- GISPA(feature=1, f.sets=c(exprset), g.set=NULL, ref.samp.idx=1, comp.samp.idx=c(2,3), f.profiles=c("up"), cpt.data="var", cpt.method="BinSeg", cpt.max=5) head(results) ## ---- message=F, warning=F, eval=F--------------------------------------- # results <- GISPA(feature=3, f.sets=c(exprset,cnvset,varset), g.set=NULL, # ref.samp.idx=1, comp.samp.idx=c(2,3), # f.profiles=c("down", "down", "down"), # cpt.data="var", cpt.method="BinSeg", cpt.max=5) # head(results)