20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,102 @@
+
+get_Poisson_conf_intervals = function(seq_range, quantile_vec = c(0.05,0.95), plot=T) {
+	
+	num_rows = length(seq_range)
+	num_cols = length(quantile_vec)
+	m = matrix(nrow=num_rows, ncol=num_cols)
+	
+    colnames(m) = quantile_vec	
+	rownames(m) = seq_range
+
+	row_count = 0
+	for (i in seq_range) {
+		q = qpois(quantile_vec, i)
+		row_count = row_count + 1
+		m[row_count,] = q			
+	
+	}
+
+    results = list()
+    results$mat = m
+	
+	if (plot) {
+		percents = plot_conf_intervals(m)
+ 	    
+        results$pct = percents
+    }
+
+	return(results)
+
+}
+
+
+get_NB_conf_intervals = function(seq_range, dispersion, quantile_vec = c(0.05,0.95), plot=T) {
+	
+    size = 1/dispersion  #according to the mu-definition of size in nbinom of R, where var = mean + (1/size)mean^2
+    
+	num_rows = length(seq_range)
+	num_cols = length(quantile_vec)
+	m = matrix(nrow=num_rows, ncol=num_cols)
+	
+    colnames(m) = quantile_vec	
+	rownames(m) = seq_range
+
+	row_count = 0
+	for (i in seq_range) {
+		q = qnbinom(quantile_vec, mu=i, size=size)
+		row_count = row_count + 1
+		m[row_count,] = q			
+	
+	}
+	
+    results = list()
+    results$mat = m
+    
+
+	if (plot) {
+		percents = plot_conf_intervals(m)
+ 	
+        results$pct = percents
+    }
+
+	return(results)
+
+}
+
+
+
+
+
+
+plot_conf_intervals = function(m) {
+
+	par(mfrow=c(1,2))
+
+	c_names = colnames(m)
+	r_vals = as.numeric(rownames(m))
+
+	max_val = max(m)
+	
+	plot(r_vals, r_vals, xlab="known read counts", ylab="Poisson read counts dist", t='l')
+
+	# plot the confidence levels
+	line_colors = rainbow(length(c_names))
+	for(i in 1:length(c_names)) {
+		points(r_vals,m[,i], t='l', col=line_colors[i])
+	}
+
+	# plot the max percentage of value for 95% conf level.
+	percents=c()
+	for (i in 1:length(r_vals)) {
+
+		max_delta = max(abs(m[i,]-r_vals[i]))
+		percent = max_delta/r_vals[i]*100
+		
+		percents[i]=percent;
+	}
+	
+	plot(r_vals, percents, ylim=c(0,100), xlab="read counts", ylab="percent of value for 95% conf interval")
+
+	percents
+
+}