From 3c08a1c061828bc36e80177404ce84a557e4268d Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 8 Nov 2010 21:02:10 +0000
Subject: [PATCH] Basic script for assessing simulation sensitivity and
 specificity

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4638 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/assessCallingPerformance.R | 41 ++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 R/assessCallingPerformance.R

diff --git a/R/assessCallingPerformance.R b/R/assessCallingPerformance.R
new file mode 100644
index 000000000..a2b49604f
--- /dev/null
+++ b/R/assessCallingPerformance.R
@@ -0,0 +1,41 @@
+#d <- read.table("sim_calls.table", header=T)
+
+d$sim.VAR <- d$sim.AC > 0
+d$called.VAR <- d$called.AC > 0
+
+QS = unique(d$sim.Q)
+MODES = unique(d$sim.MODE)
+NS = unique(d$called.AN / 2)
+DEPTHS = unique(d$sim.DP)
+
+results <- expand.grid(Q = QS, mode = MODES, nSamples = NS, depth = DEPTHS)
+results$sensitivity = 0
+results$specificity = 0
+
+determineRates <- function(raw, Q, mode, depth) {
+    sub <- subset(raw, sim.Q == Q & sim.MODE == mode & sim.DP == depth)
+    ct <- table(sub$called.VAR, sub$sim.VAR, dnn = c("called.VAR", "sim.VAR"))
+    sensitivity = ct[2,2] / sum(ct[,2]) 
+    specificity = ct[1,1] / sum(ct[,1])
+    list(sensitivity = sensitivity, specificity = specificity, ct = ct)
+}
+
+for ( i in 1:(dim(results)[1]) ) {
+    r <- results[i,]
+    x <- determineRates(d, r$Q, r$mode, r$depth)
+    results[i,]$sensitivity = x$sensitivity
+    results[i,]$specificity = x$specificity
+}
+
+for ( depth in DEPTHS ) 
+    boxplot(called.AC ~ sim.AC, data = subset(d, called.DP == depth * NS), main = paste("Depth of coverage ", depth), xlab = "Simulation AC", ylab = "Called AC")
+
+print(results)
+
+par(mfcol=c(2,1))
+for ( Qt in QS ) {
+    x <- subset(results, Q == Qt)
+    print(x)
+    plot(x$depth, x$sensitivity, type="b")
+    plot(x$depth, x$specificity, type="b")
+}