## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set(collapse = TRUE, cache = FALSE, comment = "#>") ## ----packageLoad, message=FALSE----------------------------------------------- library(tidyverse) library(pathwayPCA) ## ----tumour_data_load--------------------------------------------------------- data("colonSurv_df") colonSurv_df ## ----pathway_list_load-------------------------------------------------------- data("colon_pathwayCollection") colon_pathwayCollection str(colon_pathwayCollection$pathways, list.len = 10) ## ----data_types--------------------------------------------------------------- # Original integer column head(colonSurv_df$OS_event, 10) # Integer to Character head(as.character(colonSurv_df$OS_event), 10) # Integer to Logical head(as.logical(colonSurv_df$OS_event), 10) # Integer to Factor head(as.factor(colonSurv_df$OS_event), 10) ## ----create_OmicsSurv_object-------------------------------------------------- colon_OmicsSurv <- CreateOmics( assayData_df = colonSurv_df[, -(2:3)], pathwayCollection_ls = colon_pathwayCollection, response = colonSurv_df[, 1:3], respType = "surv" ) ## ----print_colonOmicsSurv----------------------------------------------------- colon_OmicsSurv ## ----create_OmicsReg_object--------------------------------------------------- colon_OmicsReg <- CreateOmics( assayData_df = colonSurv_df[, -(2:3)], pathwayCollection_ls = colon_pathwayCollection, response = colonSurv_df[, 1:2], respType = "reg" ) colon_OmicsReg ## ----create_OmicsCateg_object------------------------------------------------- colon_OmicsCateg <- CreateOmics( assayData_df = colonSurv_df[, -(2:3)], pathwayCollection_ls = colon_pathwayCollection, response = colonSurv_df[, c(1, 3)], respType = "categ" ) colon_OmicsCateg ## ----getAssay_get------------------------------------------------------------- getAssay(colon_OmicsSurv) ## ----getAssay_set------------------------------------------------------------- getAssay(colon_OmicsSurv) <- colonSurv_df[, (3:12)] ## ----view_new_colon_OS-------------------------------------------------------- colon_OmicsSurv ## ----getAssay_set2------------------------------------------------------------ getAssay(colon_OmicsSurv) <- colonSurv_df[, -(1:2)] ## ----inspect_updated_pathwayCollection---------------------------------------- getPathwayCollection(colon_OmicsSurv) ## ----sessionDetails----------------------------------------------------------- sessionInfo()