## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----quickYo, eval = FALSE---------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("iPath") ## ----load_data, eval = TRUE, message=FALSE, results='hide', include = TRUE---- library(iPath) data(PRAD_data) dim(prad_exprs) data(GSDB_example) head(prad_cli) ## ----cal_iES2, eval = TRUE, message=FALSE, results='hide', include = TRUE----- iES_mat = iES_cal2(Y = prad_exprs, GSDB = GSDB_example) iES_mat[1:2, 1:4] ## ----survival, eval = TRUE, message=FALSE, include = TRUE--------------------- surv_outcomes = iES_surv(iES_mat = iES_mat, cli = prad_cli, indVec = prad_inds) head(surv_outcomes) ## ----waterfall, eval = TRUE, message=FALSE, include = TRUE-------------------- water_fall(iES_mat, gs_str = "SimPathway2", indVec = prad_inds) density_fall(iES_mat, gs_str = "SimPathway2", indVec = prad_inds) ## ----onesurvival, eval = TRUE, message=FALSE, include = TRUE------------------ iES_survPlot(iES_mat = iES_mat, cli = prad_cli, gs_str = "SimPathway1", indVec = prad_inds, title = TRUE) ## ----------------------------------------------------------------------------- sessionInfo()