## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set(collapse = TRUE, cache = FALSE, comment = "#>") ## ----packLoad, message=FALSE-------------------------------------------------- library(parallel) library(tidyverse) library(pathwayPCA) ## ----data_setup, echo = FALSE, message = FALSE-------------------------------- data("colonSurv_df") data("colon_pathwayCollection") colon_OmicsSurv <- CreateOmics( assayData_df = colonSurv_df[, -(2:3)], pathwayCollection_ls = colon_pathwayCollection, response = colonSurv_df[, 1:3], respType = "surv" ) ## ----data_show---------------------------------------------------------------- colon_OmicsSurv ## ----------------------------------------------------------------------------- names(getPathwayCollection(colon_OmicsSurv)$pathways) ## ----------------------------------------------------------------------------- getTrimPathwayCollection(colon_OmicsSurv)$n_tested ## ----------------------------------------------------------------------------- getPathwayCollection(colon_OmicsSurv)$TERMS ## ----aes_surv_pvals----------------------------------------------------------- colonSurv_aespcOut <- AESPCA_pVals( object = colon_OmicsSurv, numReps = 0, numPCs = 2, parallel = TRUE, numCores = 2, adjustpValues = TRUE, adjustment = c("Hoch", "SidakSD") ) ## ----aes_reg_pvals, eval=FALSE------------------------------------------------ # colonReg_aespcOut <- AESPCA_pVals( # object = colon_OmicsReg, # numReps = 0, # numPCs = 2, # parallel = TRUE, # numCores = 2, # adjustpValues = TRUE, # adjustment = c("Holm", "BH") # ) ## ----aes_categ_pvals, eval=FALSE---------------------------------------------- # colonCateg_aespcOut <- AESPCA_pVals( # object = colon_OmicsCateg, # numReps = 0, # numPCs = 2, # parallel = TRUE, # numCores = 2, # adjustpValues = TRUE, # adjustment = c("SidakSS", "BY") # ) ## ----super_surv_pvals, eval=FALSE--------------------------------------------- # colonSurv_superpcOut <- SuperPCA_pVals( # object = colon_OmicsSurv, # numPCs = 2, # parallel = TRUE, # numCores = 2, # adjustpValues = TRUE, # adjustment = c("Hoch", "SidakSD") # ) ## ----super_reg_pvals, eval=FALSE---------------------------------------------- # colonReg_superpcOut <- SuperPCA_pVals( # object = colon_OmicsReg, # numPCs = 2, # parallel = TRUE, # numCores = 2, # adjustpValues = TRUE, # adjustment = c("Holm", "BH") # ) ## ----super_categ_pvals, eval=FALSE-------------------------------------------- # colonCateg_superpcOut <- SuperPCA_pVals( # object = colon_OmicsCateg, # numPCs = 2, # parallel = TRUE, # numCores = 2, # adjustpValues = TRUE, # adjustment = c("SidakSS", "BY") # ) ## ----viewPathwayRanks--------------------------------------------------------- getPathpVals(colonSurv_aespcOut) ## ----getPathPCLs-------------------------------------------------------------- PCLs_ls <- getPathPCLs(colonSurv_aespcOut, "KEGG_ASTHMA") PCLs_ls ## ----HLARDA------------------------------------------------------------------- PCLs_ls$Loadings %>% filter(PC1 != 0) %>% select(-PC2) %>% arrange(desc(PC1)) ## ----sessionDetails----------------------------------------------------------- sessionInfo()