[Seqinr-commits] r1902 - pkg/man

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

Author: jeanlobry
Date: 2016-06-02 16:27:43 +0200 (Thu, 02 Jun 2016)
New Revision: 1902

Modified:
   pkg/man/zscore.Rd
Log:
documentation bug fix and UTF-8

Modified: pkg/man/zscore.Rd
===================================================================
--- pkg/man/zscore.Rd	2016-06-02 14:11:38 UTC (rev 1901)
+++ pkg/man/zscore.Rd	2016-06-02 14:27:43 UTC (rev 1902)
@@ -3,7 +3,7 @@
 \alias{zscore}
 \title{Statistical over- and under- representation of dinucleotides in a
   sequence}
-\encoding{latin1}
+\encoding{UTF-8}
 \description{
   These two functions compute two different types of statistics for the
   measure of statistical dinculeotide over- and under-representation :
@@ -34,9 +34,12 @@
   nucleotide \emph{x} and nucleotide \emph{y}. It is equal to 1.00 when
   dinucleotide \emph{xy} is formed by pure chance, and it is superior
   (respectively inferior) to 1.00 when dinucleotide \emph{xy} is over-
-  (respectively under-) represented.
+  (respectively under-) represented. Note that if you want to reproduce
+  Karlin's results you have to compute the statistic from the sequence 
+  concatenated with its inverted complement that is with something 
+  like \code{rho(c(myseq, rev(comp(mysed))))}.
 
-  The \code{zscore} statistic, as presented in Palmeira, L., Guéguen, L.
+  The \code{zscore} statistic, as presented in Palmeira, L., Guéguen, L.
   and Lobry JR. (2006). The statistic is the normalization of the
   \code{rho} statistic by its expectation and variance according to a
   given random sequence generation model, and follows the
@@ -49,7 +52,7 @@
   The \code{base} model allows for random sequence generation by
   shuffling (with/without replacement) of all bases in the sequence.
   Analytical computations are available for this model: either as an 
-  approximation for large sequences (cf. Palmeira, L., Guéguen, L.
+  approximation for large sequences (cf. Palmeira, L., Guéguen, L.
   and Lobry JR. (2006)), either as the exact analytical formulae
   (cf. Schbath, S. (1995)).
 
@@ -76,12 +79,12 @@
   Karlin S. and Cardon LR. (1994) Computational DNA sequence analysis.
   \emph{Annu Rev Microbiol}, \bold{48}:619-654.
 
-  Schbath, S. (1995) Étude asymptotique du nombre d'occurrences d'un
-  mot dans une chaîne de Markov et application à la recherche de mots
-  de fréquence exceptionnelle dans les séquences d'ADN.
-  \emph{Thèse de l'Université René Descartes, Paris V}
+  Schbath, S. (1995) Étude asymptotique du nombre d'occurrences d'un
+  mot dans une chaîne de Markov et application à la recherche de mots
+  de fréquence exceptionnelle dans les séquences d'ADN.
+  \emph{Thèse de l'Université René Descartes, Paris V}
 
-  Palmeira, L., Guéguen, L. and Lobry, J.R. (2006) UV-targeted dinucleotides
+  Palmeira, L., Guéguen, L. and Lobry, J.R. (2006) UV-targeted dinucleotides
   are not depleted in light-exposed Prokaryotic genomes.
   \emph{Molecular Biology and Evolution},
   \bold{23}:2214-2219.