## ----setup, echo=FALSE, results="hide"---------------------------------------- knitr::opts_chunk$set(tidy = FALSE, cache = FALSE, dev = "png", message = FALSE, error = FALSE, warning = FALSE) ## ----------------------------------------------------------------------------- library(epistasisGA) data(case.mci) case <- as.matrix(case.mci) data(dad.mci) dad <- as.matrix(dad.mci) data(mom.mci) mom <- as.matrix(mom.mci) data(snp.annotations.mci) ## ----------------------------------------------------------------------------- pseudo.sib <- mom + dad - case ## ----------------------------------------------------------------------------- input.case <- cbind(case[ , 1:6], mom[ , 1:6], case[ , 7:12], mom[ , 7:12], case[ , 13:18], mom[ , 13:18], case[ , 19:24], mom[ , 19:24]) ## ----------------------------------------------------------------------------- input.control <- cbind(pseudo.sib[ , 1:6], dad[ , 1:6], pseudo.sib[ , 7:12], dad[ , 7:12], pseudo.sib[ , 13:18], dad[ , 13:18], pseudo.sib[ , 19:24], dad[ , 19:24]) ## ----------------------------------------------------------------------------- ld.block.vec <- rep(12, 4) ## ----------------------------------------------------------------------------- pp.list <- preprocess.genetic.data(case.genetic.data = input.case, complement.genetic.data = input.control, ld.block.vec = ld.block.vec, child.snps = c(1:6, 13:18, 25:30, 37:42), mother.snps = c(7:12, 19:24, 31:36, 43:48)) ## ----message = FALSE---------------------------------------------------------- run.gadgets(pp.list, n.chromosomes = 5, chromosome.size = 3, results.dir = "size3_res", cluster.type = "interactive", registryargs = list(file.dir = "size3_reg", seed = 1300), n.islands = 8, island.cluster.size = 4, n.migrations = 2) run.gadgets(pp.list, n.chromosomes = 5, chromosome.size = 4, results.dir = "size4_res", cluster.type = "interactive", registryargs = list(file.dir = "size4_reg", seed = 1400), n.islands = 8, island.cluster.size = 4, n.migrations = 2) ## ----------------------------------------------------------------------------- snp.anno <- snp.annotations.mci[c(rep(1:6, 2), rep(7:12, 2), rep(13:18, 2), rep(19:24, 2)), ] size3.combined.res <- combine.islands("size3_res", snp.anno, pp.list) size4.combined.res <- combine.islands("size4_res", snp.anno, pp.list) ## ----------------------------------------------------------------------------- library(magrittr) library(knitr) library(kableExtra) kable(head(size3.combined.res)) %>% kable_styling() %>% scroll_box(width = "750px") ## ----------------------------------------------------------------------------- top.snps <- as.vector(t(size3.combined.res[1, 1:3])) set.seed(10) epi.test.res <- epistasis.test(top.snps, pp.list, maternal.fetal.test = TRUE) epi.test.res$pval ## ----fig.width = 14, fig.height = 12------------------------------------------ obs.res.list <- list(size3.combined.res, size4.combined.res) set.seed(10) graphical.scores <- compute.graphical.scores(obs.res.list, pp.list) network.plot(graphical.scores, pp.list, graph.area = 200, node.size = 40, vertex.label.cex = 2, node.shape = c("circle", "square")) ## ----results="hide"----------------------------------------------------------- #remove all example directories lapply(c("size3_res", "size3_reg", "size4_res", "size4_reg"), unlink, recursive = TRUE) ## ----------------------------------------------------------------------------- #session information sessionInfo()