many changes!

[ape.git] / R / DNA.R

diff --git a/R/DNA.R b/R/DNA.R
index 1f4f5d6ae78e8367635651d4507a126594a581f6..a7285170ec3aef68cf4874043ae6386edd034d30 100644 (file)
--- a/R/DNA.R
+++ b/R/DNA.R
@@ -1,4 +1,4 @@
-## DNA.R (2010-07-14)
+## DNA.R (2010-09-01)
 
 ##   Manipulations and Comparisons of DNA Sequences
 
@@ -291,6 +291,37 @@ base.freq <- function(x, freq = FALSE)
     BF
 }
 
+Ftab <- function(x, y = NULL)
+{
+    if (is.null(y)) {
+        if (is.list(x)) {
+            y <- x[[2]]
+            x <- x[[1]]
+            if (length(x) != length(y))
+                stop("'x' and 'y' not of same lenght")
+        } else { # 'x' is a matrix
+            y <- x[2, , drop = TRUE]
+            x <- x[1, , drop = TRUE]
+        }
+    } else {
+        x <- as.vector(x)
+        y <- as.vector(y)
+        if (length(x) != length(y))
+            stop("'x' and 'y' not of same lenght")
+    }
+    out <- matrix(0, 4, 4)
+    k <- c(136, 40, 72, 24)
+    for (i in 1:4) {
+        a <- x == k[i]
+        for (j in 1:4) {
+            b <- y == k[j]
+            out[i, j] <- sum(a & b)
+        }
+    }
+    dimnames(out)[1:2] <- list(c("a", "c", "g", "t"))
+    out
+}
+
 GC.content <- function(x) sum(base.freq(x)[2:3])
 
 seg.sites <- function(x)