X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fbase.freq.Rd;h=56a5e2e7f39774a22eff64aea8cba6e84de2b399;hb=40eeb40e48bccc220826860ce0ada4521cbc0148;hp=3847d9cf20c522fc1893048815fd00a76dfe7059;hpb=c827059eeafc8cbe41c812b26979543ab287803e;p=ape.git

diff --git a/man/base.freq.Rd b/man/base.freq.Rd
index 3847d9c..56a5e2e 100644
--- a/man/base.freq.Rd
+++ b/man/base.freq.Rd
@@ -1,30 +1,55 @@
 \name{base.freq}
 \alias{base.freq}
+\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{Ftab} computes the contingency table with the absolute
+  frequencies of the DNA bases from a pair of sequences.
+}
 \usage{
-base.freq(x)
+base.freq(x, freq = FALSE, all = FALSE)
+Ftab(x, y = NULL)
 }
 \arguments{
   \item{x}{a vector, a matrix, or a list which contains the DNA
     sequences.}
-}
-\description{
-  This function computes the relative frequencies (i.e. percentages) of
-  the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
-  sample of 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).}
+  \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.
+
+  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 stoting the relative frequencies with names
-  \code{c("a", "c", "g", "t")}.
+  A numeric vector with names \code{c("a", "c", "g", "t")}, or a four by
+  four matrix with similar dimnames.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link{GC.content}}, \code{\link{seg.sites}},
   \code{\link{nuc.div}}, \code{\link{DNAbin}}
 }
+\examples{
+data(woodmouse)
+base.freq(woodmouse)
+base.freq(woodmouse, TRUE)
+Ftab(woodmouse)
+Ftab(woodmouse[1, ], woodmouse[2, ]) # same than above
+Ftab(woodmouse[14:15, ]) # between the last two
+}
 \keyword{univar}
+\keyword{manip}