[Seqinr-commits] r2120 - in pkg: R man

[noreply at r-forge.r-project.org]

Author: simonpenel
Date: 2021-05-20 09:56:36 +0200 (Thu, 20 May 2021)
New Revision: 2120

Modified:
   pkg/R/dist.alignment.R
   pkg/man/dist.alignment.Rd
Log:
Now identity is the default in dist.alignment

Modified: pkg/R/dist.alignment.R
===================================================================
--- pkg/R/dist.alignment.R	2021-05-19 06:57:44 UTC (rev 2119)
+++ pkg/R/dist.alignment.R	2021-05-20 07:56:36 UTC (rev 2120)
@@ -2,7 +2,7 @@
 # Pairwise Distances from Aligned Protein or DNA/RNA Sequences
 #
 
-dist.alignment <- function(x, matrix = c("similarity", "identity"),gap )
+dist.alignment <- function(x, matrix = c("identity", "similarity"),gap )
 {
   #
   # Check arguments:

Modified: pkg/man/dist.alignment.Rd
===================================================================
--- pkg/man/dist.alignment.Rd	2021-05-19 06:57:44 UTC (rev 2119)
+++ pkg/man/dist.alignment.Rd	2021-05-20 07:56:36 UTC (rev 2120)
@@ -2,8 +2,8 @@
 \alias{dist.alignment}
 \title{ Pairwise Distances from Aligned Protein or DNA/RNA Sequences }
 \description{
-  These functions compute a matrix of pairwise distances from aligned sequences 
-  using similarity (Fitch matrix, for protein sequences only) or identity matrix 
+  These functions compute a matrix of pairwise distances from aligned sequences
+  using similarity (Fitch matrix, for protein sequences only) or identity matrix
   (for protein and DNA sequences).
   The resulting matrix contains the squared root of the pairwise distances.
   For example, if identity between 2 sequences is 80%, the matrix will gives
@@ -11,21 +11,21 @@
 
 }
 \usage{
-dist.alignment(x, matrix = c("similarity", "identity"),gap)
+dist.alignment(x, matrix = c("identity", "similarity"),gap)
 }
 \arguments{
-  \item{x}{an object of class \code{alignment}, as returned by 
+  \item{x}{an object of class \code{alignment}, as returned by
   \code{read.alignment} for instance}
   \item{matrix}{the matrix distance to be used, partial matching allowed }
   \item{gap}{-optional- with nucleotides, if set to 1, gaps will be counted in the identity measure }
 }
 \value{
-  The distance matrix, object of class \code{dist}, computed by using the 
+  The distance matrix, object of class \code{dist}, computed by using the
   specified distance measure.
 }
-\references{ 
+\references{
 The reference for the similarity matrix is :\cr
-Fitch, W.M. (1966) An improved method of testing for evolutionary homology. 
+Fitch, W.M. (1966) An improved method of testing for evolutionary homology.
 \emph{J. Mol. Biol.}, \bold{16}:9-16.\cr
 
 \code{citation("seqinr")}
@@ -33,7 +33,7 @@
 \author{D. Charif, J.R. Lobry}
 \seealso{  \code{\link{read.alignment} } }
 \examples{
- myseqs <- read.alignment(file = system.file("sequences/test.mase", 
+ myseqs <- read.alignment(file = system.file("sequences/test.mase",
  package = "seqinr"), format = "mase")
  dist.alignment(myseqs, matrix = "identity" )
  as.matrix(dist.alignment(myseqs, matrix = "identity" ))