mutolisp · May 27, 2013 10:39 · May 27, 2013
diff --git a/RRTscript.r b/RRTscript.r
@@ -0,0 +1,21 @@
+setwd("/Users/easss/Desktop/RRTbatch/")
+
+library(ape)
+library(pegas)
+# list file in current directory, where the file is end with .phy
+filelist <- list.files(path=".", pattern=".phy$")
+# create a container to store output data
+out_tab <- matrix(0, nrow=length(filelist), ncol=3)
+colnames(out_tab) <- c("dna_seq", "Chi", "Pval")
+
+i = 1
+for ( f in filelist ) { 
+    seq3 <- read.dna(f)
+    out_tab[i,1] <- f
+    out_tab[i,2] <- rr.test(x = seq3[2,], y = seq3[3, ], out = seq3[1, ])$Chi
+    out_tab[i,3] <- rr.test(x = seq3[2,], y = seq3[3, ], out = seq3[1, ])$Pval
+    i=i+1
+}
+
+# write output table
+write.table(out_tab, file="out_tab.csv", sep=",", row.names=F)