Merge pull request #265 from NBISweden/hypothesis-testing-challenge

Add draft code

hypothesis-testing-challenge/draft-code-from-payam.r

@@ -0,0 +1,60 @@
+set.seed(12) # for reproducibility
+n <- 100 # number of subjects
+n_variables <- 100 # total variables
+n_de <- 20 # number of differentially expressed variables
+n_de_age <- 5 # DE variables affected by age
+mean_random<-20 # mean of random data
+
+# Simulate subject data
+subjects <- data.frame(
+  subject_id = 1:n,
+  age = rnorm(n, 50, 10), # assuming age follows a normal distribution
+  group = factor(ifelse(runif(n) > 0.5, "Treatment", "Control"))
+)
+
+truth_random <- seq((n_de + 1),n_variables)
+truth_DE_not_age_affected<-1:(n_de - n_de_age)
+truth_DE_age_affected <- (n_de - n_de_age + 1):n_de
+
+variable_data <- matrix(nrow = n, ncol = n_variables)
+
+# Simulate random data
+for(i in seq((n_de + 1),n_variables))
+{
+  for(gr in unique(subjects$group))
+  {
+    variable_data[subjects$group==gr,i]<-rnorm(sum(subjects$group==gr),mean = mean_random)
+  }
+}
+
+# Simulate DE Variables Not Affected by Age 
+for (i in 1:(n_de - n_de_age)) {
+  variable_data[, i] <- rnorm(n, ifelse(subjects$group == "Control", mean_random, mean_random+i), 1)
+}
+
+# Simulate DE Variables Affected by Age 
+for (i in (n_de - n_de_age + 1):n_de) {
+  variable_data[, i] <- subjects$age + rnorm(n, ifelse(subjects$group == "Control", 0, 1), 0.3)
+}
+
+
+## test results
+
+library(ggvenn)
+
+### only t-test without p-value correction
+
+ggvenn(list(DE=which(sapply(as.data.frame(variable_data),function(x){t.test(x~subjects$group)$p.value})<0.05),
+                  truth_random=truth_random,truth_DE_not_age_affected=truth_DE_not_age_affected,truth_DE_age_affected=truth_DE_age_affected))
+
+### only t-test with p-value correction
+
+ggvenn(list(DE=which(p.adjust(sapply(as.data.frame(variable_data),function(x){t.test(x~subjects$group)$p.value}))<0.05),
+            truth_random=truth_random,truth_DE_not_age_affected=truth_DE_not_age_affected,truth_DE_age_affected=truth_DE_age_affected))
+
+### lm adjust with p-value correction
+
+ggvenn(list(DE=which(p.adjust(sapply(as.data.frame(variable_data),function(x){summary(lm(x~subjects$group+subjects$age))$coefficients[2,"Pr(>|t|)"]}))<0.05),
+            truth_random=truth_random,truth_DE_not_age_affected=truth_DE_not_age_affected,truth_DE_age_affected=truth_DE_age_affected))
+
+