From bf1adece8aeb48e136085233d2f5ff2f9600eaf5 Mon Sep 17 00:00:00 2001
From: Mike Vink <mike1994vink@gmail.com>
Date: Sun, 2 May 2021 17:33:26 +0200
Subject: update

---
 scripts/sam.R | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 scripts/sam.R

(limited to 'scripts/sam.R')

diff --git a/scripts/sam.R b/scripts/sam.R
new file mode 100644
index 0000000..d94794d
--- /dev/null
+++ b/scripts/sam.R
@@ -0,0 +1,49 @@
+library(samr)
+library(tidyverse)
+
+# assumes modelling exploration is loaded in the R session
+data1_sam <- data1 %>%
+    select(donor_id, outcome, Feature, value) %>%
+    mutate(outcome = factor(outcome, labels = c(1, 2))) %>%
+    pivot_wider(
+                names_from = Feature,
+                values_from = value
+                ) %>%
+    select(-donor_id)
+
+data1_sam_y <- data1_sam[['outcome']]
+data1_sam_x <- t(as.data.frame(data1_sam[-1]))
+
+samobj1 <- samr::SAM(
+           data1_sam_x,
+           data1_sam_y,
+           resp.type="Two class unpaired",
+           fdr.output = 0.5,
+           nperms = 1000,
+           genenames = rownames(data1_sam_x)
+)
+samobj1
+
+
+############# DATASET 2
+data2_sam <- data2 %>%
+    select(donor_id, outcome, Feature, value) %>%
+    mutate(outcome = factor(outcome, labels = c(1, 2))) %>%
+    pivot_wider(
+                names_from = Feature,
+                values_from = value
+                ) %>%
+    select(-donor_id)
+
+data2_sam_y <- data2_sam[['outcome']]
+data2_sam_x <- t(as.data.frame(data2_sam[-1]))
+
+samobj2 <- samr::SAM(
+           data2_sam_x,
+           data2_sam_y,
+           resp.type="Two class unpaired",
+           fdr.output = 0.01,
+           nperms = 1000,
+           genenames = rownames(data2_sam_x)
+)
+samobj2
-- 
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