## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set(collapse = TRUE, cache = FALSE, comment = "#>") ## ----packageLoad, message=FALSE----------------------------------------------- library(tidyverse) # Set tibble data frame print options options(tibble.max_extra_cols = 10) library(pathwayPCA) ## ----read_gmt----------------------------------------------------------------- gmt_path <- system.file("extdata", "c2.cp.v6.0.symbols.gmt", package = "pathwayPCA", mustWork = TRUE) cp_pathwayCollection <- read_gmt(gmt_path, description = TRUE) ## ----pathwayCollection_structure---------------------------------------------- cp_pathwayCollection ## ----create_test_pathwayCollection-------------------------------------------- myPathways_ls <- list( pathway1 = c("Gene1", "Gene2"), pathway2 = c("Gene3", "Gene4", "Gene5"), pathway3 = "Gene6" ) myPathway_names <- c( "KEGG_IMPORTANT_PATHWAY_1", "KEGG_IMPORTANT_PATHWAY_2", "SOME_OTHER_PATHWAY" ) CreatePathwayCollection( sets_ls = myPathways_ls, TERMS = myPathway_names, website = "URL_TO_PATHWAY_CITATION" ) ## ----write_gmt, eval=FALSE---------------------------------------------------- # write_gmt( # pathwayCollection = cp_pathwayCollection, # file = "../test.gmt" # ) ## ----read_assay--------------------------------------------------------------- assay_path <- system.file("extdata", "ex_assay_subset.csv", package = "pathwayPCA", mustWork = TRUE) assay_df <- read_csv(assay_path) ## ----assay_print-------------------------------------------------------------- assay_df ## ----transpose---------------------------------------------------------------- (assayT_df <- TransposeAssay(assay_df)) ## ----subset_2ndrow------------------------------------------------------------ assayT_df[2, ] ## ----subset_3rdcol------------------------------------------------------------ assayT_df[, 3] ## ----subset_23---------------------------------------------------------------- assayT_df[2, 3, drop = TRUE] ## ----subset_3rdcol_byname----------------------------------------------------- assayT_df$LSS ## ----stdExpr_Example---------------------------------------------------------- library(SummarizedExperiment) data(airway, package = "airway") airway_df <- SE2Tidy(airway) ## ----------------------------------------------------------------------------- airway_df[, 1:20] ## ----read_pinfo--------------------------------------------------------------- pInfo_path <- system.file("extdata", "ex_pInfo_subset.csv", package = "pathwayPCA", mustWork = TRUE) pInfo_df <- read_csv(pInfo_path) ## ----pInfo-------------------------------------------------------------------- pInfo_df ## ----innerJoin---------------------------------------------------------------- joinedExperiment_df <- inner_join(pInfo_df, assayT_df, by = "Sample") joinedExperiment_df ## ----tumour_data_load--------------------------------------------------------- data("colonSurv_df") colonSurv_df ## ----pathway_list_load-------------------------------------------------------- data("colon_pathwayCollection") colon_pathwayCollection ## ----sessionDetails----------------------------------------------------------- sessionInfo()