diff scripts/S03b_sign_test_binomial.R @ 0:acc3674e515b draft default tip

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S03b_sign_test_binomial.R	Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,56 @@
+#!/usr/bin/env Rscript
+#coding: utf-8
+#Author : Eric Fontanillas (2010) - Victor Mataigne (2018)
+
+# binom test - null hypothesis : 
+# The test computes the number of times where the value of the variable A is higher to the value of the variable B.
+# Under the null hypothesis, there is no difference between variables : A > B in 50% of the trials
+
+options(warn = -1)
+
+library(optparse)
+
+option_list = list(
+  make_option(c('-i', '--indir'), type='character', default=NULL, help='input directory name', metavar='character'),
+  make_option(c('-o', '--outdir'), type='character', default=NULL, help='output directory name', metavar='character')
+);
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+path_IN <- opt$indir
+path_OUT <- opt$outdir
+files_OUT <- paste(path_OUT,"/*",sep='')
+unlink(files_OUT)  ### clean the path_OUT folder from previous files
+list_files <- list.files(path_IN)
+
+# iterate over file
+for(file in list_files){
+    name_OUT = paste(path_OUT,"/", file, sep='')    
+    name_IN = paste(path_IN,"/", file, sep='')
+
+    b <- read.table(name_IN, sep=",", header=T, row.names=1)
+
+    supplemental_cells <- matrix(0, nrow=4, ncol=ncol(b))
+    colnames(supplemental_cells) <- colnames(b)
+    row.names(supplemental_cells) <- c('p-value', 'probability_of_success', 'confidence_interval_low', 'confidence_interval_high')
+
+    # iterate over species groups
+    for (i in 1:ncol(b)) {
+      if (b[4,i] != 0) {
+        binom_test <- binom.test(b[1,i], b[4,i])
+        supplemental_cells[1,i] <- binom_test$p.value
+        supplemental_cells[2,i] <- binom_test$estimate
+        supplemental_cells[3,i] <- binom_test$conf.int[1]
+        supplemental_cells[4,i] <- binom_test$conf.int[2]
+      } else {
+        supplemental_cells[1,i] <- NA
+        supplemental_cells[2,i] <- NA      
+        supplemental_cells[3,i] <- NA
+        supplemental_cells[4,i] <- NA
+      }
+    }
+
+    final <- rbind(b, supplemental_cells)
+    write.csv(final, file=name_OUT)
+}
+