[Seqinr-commits] r2047 - pkg/man

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

Author: jeanlobry
Date: 2017-07-03 19:36:31 +0200 (Mon, 03 Jul 2017)
New Revision: 2047

Modified:
   pkg/man/kaks.Rd
Log:
adding the new argument rmgap to kaks

Modified: pkg/man/kaks.Rd
===================================================================
--- pkg/man/kaks.Rd	2017-07-03 17:36:07 UTC (rev 2046)
+++ pkg/man/kaks.Rd	2017-07-03 17:36:31 UTC (rev 2047)
@@ -4,7 +4,7 @@
 \description{ Ks and Ka  are, respectively, the number of substitutions per synonymous site and per non-synonymous site between two protein-coding genes. They are also denoted as ds and dn in the literature. The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitution rates is an indicator of selective pressures on genes. A ratio significantly greater than 1 indicates positive selective pressure. A ratio around 1 indicates either neutral evolution at the protein level or an averaging of sites under positive and negative selective pressures. A ratio less than 1 indicates pressures to conserve protein sequence (\emph{i.e.} purifying selection). This function estimates the Ka and Ks values for a set of aligned sequences using the method published by Li (1993) and gives the associated variance matrix. 
 }
 \usage{
-kaks(x,verbose = FALSE, debug = FALSE,  forceUpperCase = TRUE)
+kaks(x, verbose = FALSE, debug = FALSE, forceUpperCase = TRUE, rmgap = TRUE)
 }
 \arguments{
   \item{x}{ An object of class \code{alignment}, obtained for instance by importing into R the data from an alignment file with the \code{\link{read.alignment}} function. This is typically a set of coding sequences aligned at the protein level, see \code{\link{reverse.align}}.}
@@ -13,6 +13,7 @@
   \item{forceUpperCase}{ If TRUE, the default value, all character in sequences are forced to the upper case
   if at least one 'a', 'c', 'g', or 't' is found in the sequences. 
   Turning it to FALSE if the sequences are already in upper case will save time.}
+  \item{rmgap}{ If TRUE all positions with at least one gap are removed. If FALSE only positions with nothing else than gaps are removed.}
 }
 \value{
   \item{ ks }{ matrix of Ks values }