## ----load, eval=TRUE, echo=T, message=FALSE, warning=FALSE-------------------- library(EpiDISH) data(centEpiFibIC.m) data(DummyBeta.m) ## ----infer, eval=TRUE, echo=T, message=FALSE, warning=FALSE------------------- out.l <- epidish(beta.m = DummyBeta.m, ref.m = centEpiFibIC.m, method = "RPC") ## ----check, eval=TRUE, echo=T, message=FALSE, warning=FALSE------------------- out.l$estF dim(out.l$ref) dim(out.l$dataREF) ## ----inferBlood, eval=TRUE, echo=T, message=FALSE, warning=FALSE-------------- data(LiuDataSub.m) BloodFrac.m <- epidish(beta.m = LiuDataSub.m, ref.m = centDHSbloodDMC.m, method = "RPC")$estF ## ----boxplot, eval=TRUE, echo=T, message=FALSE, warning=FALSE, fig.height = 5, fig.width = 8, fig.align = "center"---- boxplot(BloodFrac.m) ## ----hepidish, eval=TRUE, echo=T, message=FALSE, warning=FALSE---------------- data(centBloodSub.m) frac.m <- hepidish(beta.m = DummyBeta.m, ref1.m = centEpiFibIC.m, ref2.m = centBloodSub.m[,c(1, 2, 5)], h.CT.idx = 3, method = 'RPC') frac.m ## ----celldmc, eval=TRUE, echo=T, message=FALSE, warning=FALSE----------------- pheno.v <- rep(c(0, 1), each = 5) celldmc.o <- CellDMC(DummyBeta.m, pheno.v, frac.m) ## ----dmct, eval=TRUE, echo=T, message=FALSE, warning=FALSE-------------------- head(celldmc.o$dmct) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()