## ----------------------------------------------------------------------------- exp_data <- rnorm(100) names(exp_data) <- paste("sample", 1:100) groupA.labels <- rep("A",50) groupB.labels <- rep("B",20) groupC.labels <- rep("C",30) labels <- c(groupA.labels, groupB.labels, groupC.labels) names(labels) <- names(exp_data) ## ----------------------------------------------------------------------------- library(ggplot2) df <- as.data.frame(exp_data) df$group[1:50] <- "A" df$group[51:70] <- "B" df$group[71:100] <- "C" ggplot(df, aes(exp_data, fill=group)) + geom_density(alpha=0.5) ## ----------------------------------------------------------------------------- library(EMDomics) calculate_emd_gene(exp_data, labels, names(exp_data)) ## ----------------------------------------------------------------------------- exp_data2 <- exp_data mod_vec <- sample(c(2,-2), 50, replace=TRUE) exp_data2[1:50] <- exp_data2[1:50] + mod_vec ## ----------------------------------------------------------------------------- df <- as.data.frame(exp_data2) df$group[1:50] <- "A" df$group[51:70] <- "B" df$group[71:100] <- "C" ggplot(df, aes(exp_data2, fill=group)) + geom_density(alpha=0.5) calculate_emd_gene(exp_data2, labels, names(exp_data2)) ## ----------------------------------------------------------------------------- data <- matrix(rnorm(10000), nrow=100, ncol=100) rownames(data) <- paste("gene", 1:100, sep="") colnames(data) <- paste("sample", 1:100, sep="") groupA.labels <- rep("A",50) groupB.labels <- rep("B",20) groupC.labels <- rep("C",30) labels <- c(groupA.labels, groupB.labels, groupC.labels) names(labels) <- colnames(data) ## ----message=FALSE------------------------------------------------------------ results <- calculate_emd(data, labels, nperm=10, parallel=FALSE) ## ----------------------------------------------------------------------------- emd <- results$emd head(emd) ## ----------------------------------------------------------------------------- emd2 <- emd[(order(emd[,"q-value"])),] head(emd2) ## ----------------------------------------------------------------------------- emd.pairwise <- results$pairwise.emd.table head(emd.pairwise) ## ----------------------------------------------------------------------------- emd3 <- emd[(order(emd[,"emd"])),] smallest_gene <- rownames(emd3)[1] biggest_gene <- rownames(emd3)[nrow(emd3)] plot_emd_density(results, smallest_gene) plot_emd_density(results, biggest_gene) ## ----message=FALSE------------------------------------------------------------ plot_emdperms(results) ## ----------------------------------------------------------------------------- plot_emdnull(results) ## ----echo=FALSE--------------------------------------------------------------- sessionInfo()