## ----setup, include = FALSE--------------------------------------------------- library(knitr) # knitr::opts_knit$set(root.dir = normalizePath("/Users/mbuljan/Documents/Paket_op/DominoEffect_radna/inst/doc")) #library(devtools) #knitr::opts_knit$set(root.dir = normalizePath(inst("DominoEffect"))) ## ---- eval=FALSE-------------------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("DominoEffect") ## ----------------------------------------------------------------------------- library(DominoEffect) ## ----------------------------------------------------------------------------- data("TestData", package = "DominoEffect") data("SnpData", package = "DominoEffect") data("DominoData", package = "DominoEffect") ## ---- eval=FALSE-------------------------------------------------------------- # DominoEffect(TestData, DominoData, SnpData) ## ---- eval=FALSE-------------------------------------------------------------- # mutation_dataset = read.table ("user_file_with_mutations.txt", header = T) # gene_data = read.table ("user_ensembl_gene_list.txt", header = T) # snp_data = read.table ("user_population_SNPs_with_frequency.txt", header = T) ## ---- message = FALSE, results = "hide"--------------------------------------- hotspot_mutations <- DominoEffect(mutation_dataset = TestData, gene_data = DominoData, snp_data = SnpData) ## ---- eval= FALSE------------------------------------------------------------- # data("TestData", package = "DominoEffect") ## ---- echo = FALSE------------------------------------------------------------ kable(head(TestData), row.names = FALSE) ## ---- echo = FALSE------------------------------------------------------------ kable(head(hotspot_mutations), row.names = FALSE) ## ---- eval = FALSE------------------------------------------------------------ # hotspot_mutations <- DominoEffect(mutation_dataset, gene_data, snp_data, min_n_muts, MAF_thresh, flanking_region, poisson.thr, percentage.thr, ratio.thr, approach, write_to_file) ## ----------------------------------------------------------------------------- min_n_muts <- 5 ## ----------------------------------------------------------------------------- MAF.thr <- 0.01 ## ----------------------------------------------------------------------------- flanking_region <- c(200, 300) flanking_region <- c(300) ## ----------------------------------------------------------------------------- poisson.thr <- 0.01 ## ----------------------------------------------------------------------------- percentage.thr <- 0.15 ## ----------------------------------------------------------------------------- ratio.thr <- 40 ## ----------------------------------------------------------------------------- approach = "percentage" ## ---- eval = FALSE------------------------------------------------------------ # write_to_file = "YES" ## ---- message = FALSE, results = "hide", eval = FALSE------------------------- # hotspot_mutations <- DominoEffect(mutation_dataset = TestData, # gene_data = DominoData, snp_data = SnpData) ## ---- message = FALSE--------------------------------------------------------- hotspot_mutations <- identify_hotspots(mutation_dataset = TestData, gene_data = DominoData, snp_data = SnpData, min_n_muts = 5, MAF_thresh = 0.01, flanking_region = c(200, 300), poisson.thr = 0.01, percentage.thr = 0.15, ratio.thr = 45, approach = "percentage") ## ---- message = FALSE, eval = FALSE------------------------------------------- # results_w_annotations <- map_to_func_elem(hotspot_mutations, # write_to_file = "NO", # ens_release = "73") ## ---- echo = FALSE------------------------------------------------------------ kable(head(DominoData), row.names = FALSE) ## ---- echo = FALSE------------------------------------------------------------ kable(head(SnpData), row.names = FALSE) ## ---- echo = FALSE------------------------------------------------------------ hotspot_mutations.GPo <- GPo_of_hotspots(hotspot_mutations) head(hotspot_mutations.GPo) ## ----------------------------------------------------------------------------- sessionInfo()