## ----setup, include=FALSE-------------------------------------------------- knitr::opts_chunk$set(dpi = 300) knitr::opts_chunk$set(cache=FALSE) ## ---- echo = FALSE,hide=TRUE, message=FALSE,warning=FALSE------------------ devtools::load_all(".") ## ---- eval = FALSE--------------------------------------------------------- # source("https://bioconductor.org/biocLite.R") # biocLite("StarBioTrek") ## ---- eval = TRUE---------------------------------------------------------- patha<-getKEGGdata(KEGG_path="Transcript") ## ---- eval = TRUE, echo = FALSE-------------------------------------------- knitr::kable(colnames(path), digits = 2, caption = "List of patwhays for the group Transcript",row.names = FALSE) ## ---- eval = TRUE---------------------------------------------------------- organism="Saccharomyces_cerevisiae" netwa<-getNETdata(network="SHpd",organism) ## ---- eval = TRUE---------------------------------------------------------- network_path<-path_net(pathway=path,data=netw) ## ---- eval = TRUE---------------------------------------------------------- list_path<-list_path_net(lista_net=network_path,pathway=path) ## ---- eval = TRUE---------------------------------------------------------- list_path_gene<-GE_matrix(DataMatrix=tumo[,1:2],pathway=path) ## ---- eval = TRUE---------------------------------------------------------- score_mean<-average(dataFilt=tumo[,1:2],pathway=path) ## ---- eval = TRUE---------------------------------------------------------- score_st_dev<-st_dv(DataMatrix=tumo[,1:2],pathway=path) ## ---- eval = TRUE---------------------------------------------------------- score_euc_dista<-euc_dist_crtlk(dataFilt=tumo[,1:2],pathway=path) ## ---- eval = TRUE---------------------------------------------------------- cross_talk_st_dv<-ds_score_crtlk(dataFilt=tumo[,1:2],pathway=path) ## ---- eval = FALSE--------------------------------------------------------- # nf <- 60 # res_class<-svm_classification(TCGA_matrix=score_euc_dist[1:2,],nfs=nf,normal=colnames(norm[,1:12]),tumour=colnames(tumo[,1:12])) ## ---- fig.width=6, fig.height=4, echo=FALSE, fig.align="center"------------ library(png) library(grid) img <- readPNG("plot_class.png") grid.raster(img) ## ---- eval = TRUE---------------------------------------------------------- DRIVER_SP<-IPPI(patha=path,netwa=netw) ## ---- fig.width=6, fig.height=4, echo=FALSE, fig.align="center"------------ library(png) library(grid) img <- readPNG("plot_path.png") grid.raster(img) ## ----sessionInfo----------------------------------------------------------- sessionInfo()