some changes for ape 3.0-6

[ape.git] / man / base.freq.Rd

diff --git a/man/base.freq.Rd b/man/base.freq.Rd
index dcb564e6329f6263eb9d1ca4f69f7708b48c7e46..8832fccf71001779e0290f7ae786d52d0caa6060 100644 (file)
--- a/man/base.freq.Rd
+++ b/man/base.freq.Rd
@@ -1,32 +1,62 @@
 \name{base.freq}
 \alias{base.freq}
+\alias{GC.content}
+\alias{Ftab}
 \title{Base frequencies from DNA Sequences}
+\description{
+  \code{base.freq} computes the frequencies (absolute or relative) of
+  the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
+  sample of sequences.
+
+  \code{GC.content} computes the proportion of G+C (using the previous
+  function). All missing or unknown sites are ignored.
+
+  \code{Ftab} computes the contingency table with the absolute
+  frequencies of the DNA bases from a pair of sequences.
+}
 \usage{
-base.freq(x, freq = FALSE)
+base.freq(x, freq = FALSE, all = FALSE)
+GC.content(x)
+Ftab(x, y = NULL)
 }
 \arguments{
   \item{x}{a vector, a matrix, or a list which contains the DNA
     sequences.}
+  \item{y}{a vector with a single DNA sequence.}
   \item{freq}{a logical specifying whether to return the proportions
     (the default) or the absolute frequencies (counts).}
-}
-\description{
-  This function computes the relative frequencies (i.e. proportions) of
-  the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
-  sample of sequences.
+  \item{all}{a logical; by default only the counts of A, C, G, and T are
+    returned. If \code{all = TRUE}, all counts of bases, ambiguous codes,
+    missing data, and alignment gaps are returned.}
 }
 \details{
   The base frequencies are computed over all sequences in the
-  sample. All missing or unknown sites are discarded from the
-  computations.
+  sample.
+
+  For \code{Ftab}, if the argument \code{y} is given then both \code{x}
+  and \code{y} are coerced as vectors and must be of equal length. If
+  \code{y} is not given, \code{x} must be a matrix or a list and only
+  the two first sequences are used.
 }
 \value{
-  A numeric vector storing the relative frequencies with names
-  \code{c("a", "c", "g", "t")}.
+  A numeric vector with names \code{c("a", "c", "g", "t")} (and possibly
+  \code{"r", "m", ...}, a single numeric value, or a four by four matrix
+  with similar dimnames.
 }
 \author{Emmanuel Paradis}
 \seealso{
-  \code{\link{GC.content}}, \code{\link{seg.sites}},
-  \code{\link{nuc.div}}, \code{\link{DNAbin}}
+  \code{\link{seg.sites}}, \code{\link[pegas]{nuc.div}},
+  \code{\link{DNAbin}}
+}
+\examples{
+data(woodmouse)
+base.freq(woodmouse)
+base.freq(woodmouse, TRUE)
+base.freq(woodmouse, TRUE, TRUE)
+GC.content(woodmouse)
+Ftab(woodmouse)
+Ftab(woodmouse[1, ], woodmouse[2, ]) # same than above
+Ftab(woodmouse[14:15, ]) # between the last two
 }
 \keyword{univar}
+\keyword{manip}