## ----echo=FALSE--------------------------------------------------------------- knitr::opts_chunk$set(fig.pos="h", out.extra='', fig.align="center") library(SEPIRA) data("GeneExp") data.m <- GeneExp dataVAL.m <- GeneExp data("TFeid") ## ----warning=F---------------------------------------------------------------- net.o <- sepiraInfNet(data=data.m, tissue=colnames(data.m), toi = "Lung", cft = "Blood", TFs = TFeid, sdth = 0.25, sigth = 0.05, pcorth = 0.2, degth = c(0.05, 0.05), lfcth = c(log2(1.5), 0), minNtgts = 5, ncores = 1) ## Note: `data.m` should be a normalized gene expression data set. ## Parameters used here are not recommended. See "?sepiraInfNet" for more info. ## ----------------------------------------------------------------------------- act <- sepiraRegAct(data = data.m, type = "DNAm", regnet = net.o$netTOI, norm = "z", ncores = 1) ## ----warning=F---------------------------------------------------------------- net.o <- sepiraInfNet(data=data.m, tissue=colnames(data.m), toi = "Lung", cft = "Blood", TFs = TFeid, sdth = 0.25, sigth = 0.05, pcorth = 0.2, degth = c(0.05, 0.05), lfcth = c(log2(1.5), 0), minNtgts = 3, ncores = 1) ## ----out.width = 400, fig.retina = NULL, echo=F------------------------------- knitr::include_graphics("Figures/LungNet_last_version.png") ## ----------------------------------------------------------------------------- # estimating transcription factor activity in data.m TFact_gtex.m <- sepiraRegAct(data.m,type="exp",regnet=net.o$netTOI,norm="z",ncores=1) ## ----out.width = 650, fig.retina = NULL, echo=F------------------------------- knitr::include_graphics("Figures/LungNet_box_GTEx.png") ## ----------------------------------------------------------------------------- # estimating transcription factor activity in a validation dataset TFact_val.m <- sepiraRegAct(dataVAL.m,type="exp",regnet=net.o$netTOI,norm="z",ncores=1) ## ----out.width = 650, fig.retina = NULL, echo=F------------------------------- knitr::include_graphics("Figures/LungNet_box_ProAtl.png") ## ----out.width = 300, fig.retina = NULL, echo=F------------------------------- knitr::include_graphics("Figures/SCM2.png") ## ----sessionInfo-------------------------------------------------------------- sessionInfo()