## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup files-------------------------------------------------------------- library(PAST) demo_association_file = system.file("extdata", "association.txt.xz", package = "PAST", mustWork = TRUE) demo_effects_file = system.file("extdata", "effects.txt.xz", package = "PAST", mustWork = TRUE) demo_LD_file = system.file("extdata", "LD.txt.xz", package = "PAST", mustWork = TRUE) demo_genes_file = system.file("extdata", "genes.gff", package = "PAST", mustWork = TRUE) demo_pathways_file = system.file("extdata", "pathways.txt.xz", package = "PAST", mustWork = TRUE) ## ----loading_gwas_data-------------------------------------------------------- gwas_data <- load_GWAS_data(demo_association_file, demo_effects_file) ## ----loading_ld_data---------------------------------------------------------- LD <- load_LD(demo_LD_file) ## ----assigning_SNPs----------------------------------------------------------- genes <-assign_SNPs_to_genes(gwas_data, LD, demo_genes_file, c("gene"), 1000, 0.8, 2) ## ----finding_pathways--------------------------------------------------------- rugplots_data <- find_pathway_significance(genes, demo_pathways_file, 5, "increasing", 1000, 2) ## ----plotting----------------------------------------------------------------- plot_pathways(rugplots_data, "pvalue", 0.02, "increasing", tempdir())