[adegenet-commits] r740 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Dec 14 16:26:04 CET 2010
Author: jombart
Date: 2010-12-14 16:26:04 +0100 (Tue, 14 Dec 2010)
New Revision: 740
Added:
www/reviewDAPC.html
Modified:
www/literature.html
www/news.html
Log:
Added review of DAPC paper by L. E.
Modified: www/literature.html
===================================================================
--- www/literature.html 2010-12-13 22:05:02 UTC (rev 739)
+++ www/literature.html 2010-12-14 15:26:04 UTC (rev 740)
@@ -107,7 +107,8 @@
<b>Jombart T</b>, Devillard S and Balloux F <b> </b>(2010)
Discriminant analysis of principal components: a new method for the
analysis of genetically structured populations. <i>BMC Genetics</i> <strong>11</strong><strong>:</strong>94.
-<span>doi:10.1186/1471-2156-11-94</span><br>
+<span>doi:10.1186/1471-2156-11-94</span> [<a href="reviewDAPC.html">evaluation
+by Laurent Excoffier on F1000</a>]<br>
<br>
<br>
<span style="text-decoration: underline;">Publications citing
@@ -334,7 +335,8 @@
Notodontidae).
Journal
of
-Evolutionary Biology, no.
+Evolutionary
+Biology, no.
doi: 10.1111/j.1420-9101.2010.02147.x<br>
</p>
<p class="auth_list">[25] Giorgia Ferrara, Rita Cannas, Marco Stagioni,
Modified: www/news.html
===================================================================
--- www/news.html 2010-12-13 22:05:02 UTC (rev 739)
+++ www/news.html 2010-12-14 15:26:04 UTC (rev 740)
@@ -4,7 +4,7 @@
<meta content="text/html; charset=ISO-8859-1"
http-equiv="content-type">
<title>news</title>
-<script type="text/javascript">
+ <script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-20083187-1']);
@@ -16,7 +16,7 @@
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
-</script>
+ </script>
</head>
<body>
<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
@@ -39,6 +39,12 @@
for a list of
all modifications.<br>
<br>
+<span style="font-weight: bold;">14/12/2010 </span><img
+ style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+<span style="font-weight: bold;">The DAPC paper has been nicely
+reviewed by Laurent Excoffier on Faculty of 1000</span> [<a
+ href="reviewDAPC.html">see evaluation</a>].<br>
+<br>
<span style="font-weight: bold;">08/11/2010 </span><span
style="font-weight: bold;"></span><img
style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
@@ -60,8 +66,8 @@
hierfstat (function <span
style="color: rgb(255, 0, 0); font-family: monospace;">genind2hierfstat</span>),
which
-lead to wrong <span
- style="font-family: monospace; color: rgb(255, 0, 0);">fstat</span>
+lead
+to wrong <span style="font-family: monospace; color: rgb(255, 0, 0);">fstat</span>
computations in some cases. See the </span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><a
href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
@@ -236,7 +242,8 @@
at
the
same
-time as the package
+time
+as the package
release!<br>
<br>
<br>
@@ -259,7 +266,8 @@
things
and
corrects
-a few bugs
+a
+few bugs
(see </span></span><a href="files/ChangeLog">ChangeLog</a><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
file). Amongst the biggest news, <span style="font-weight: bold;">several
@@ -278,7 +286,8 @@
RGB
scale,
and
-a <span style="font-family: monospace; color: rgb(255, 0, 0);">loadingplot</span>,
+a
+<span style="font-family: monospace; color: rgb(255, 0, 0);">loadingplot</span>,
which
can
be
@@ -288,7 +297,8 @@
the
most
structuring
-alleles and loci in an
+alleles
+and loci in an
analysis. A new georeferenced genetic dataset is also available
(dataset <span style="color: rgb(255, 0, 0); font-family: monospace;">rupica</span>).
And...
@@ -314,7 +324,8 @@
arising
in
version
-1.2-0 (see </span></span><a href="files/ChangeLog">ChangeLog</a><span
+1.2-0
+(see </span></span><a href="files/ChangeLog">ChangeLog</a><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
file), especially an issue with the detection of NAs. Documentation was
also improved (have a look at <span
@@ -340,7 +351,8 @@
ploidy
and
adds
-some new
+some
+new
features (see </span></span><a href="files/ChangeLog">ChangeLog</a><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
file):<br>
@@ -383,7 +395,8 @@
adds
some
new
-features (see </span></span><a href="files/ChangeLog">ChangeLog</a><span
+features
+(see </span></span><a href="files/ChangeLog">ChangeLog</a><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
file):<br>
- </span><span style="font-family: monospace;">genind2df</span></span>
@@ -421,7 +434,8 @@
of
adegenet.
It
-computes the <span style="color: rgb(255, 0, 0);">proportion
+computes
+the <span style="color: rgb(255, 0, 0);">proportion
of
shared alleles</span>
among a set of genotypes.<br>
Added: www/reviewDAPC.html
===================================================================
--- www/reviewDAPC.html (rev 0)
+++ www/reviewDAPC.html 2010-12-14 15:26:04 UTC (rev 740)
@@ -0,0 +1,97 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>documentation</title>
+ <script type="text/javascript">
+
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-20083187-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+</head>
+<body>
+<div class="evaluationBody">
+<p class="opinion">Evaluation of the DAPC paper by Laurent Excoffier on
+the <a href="http://f1000.com/">Faculty of 1000</a>:<br>
+</p>
+<p style="font-style: italic;" class="opinion">This paper elegantly
+combines a series of existing multivariate methods to detect the
+genetic structure of populations from genomic data. I found the
+validation of the methodology extremely convincing, as it shows that
+one can clearly recover very complex patterns and even hierarchical
+genetic structures.</p>
+<p style="font-style: italic;" class="mainFindingAndContext"> The
+authors propose the analysis of large genomic data sets by combining
+three model-free multivariate analysis techniques. The idea is to
+perform a discriminant analysis (DA) on genomic data, after the main
+axes of variation have been extracted by a principal component (PC)
+analysis, and genetic clusters of individuals have been identified by a
+sequential K-means and model selection method. The first use of a PC
+analysis solves two problems preventing the normal use of DA on genomic
+data. It reduces the number of genetic dimensions to a number smaller
+than that of the sampled individuals, and it ensures that information
+provided by each dimension is uncorrelated, thus removing potential
+effects of linkage disequilibrium. The Discriminant Analysis of
+Principal Components (DAPC) is blazingly fast and allows one to nicely
+visualize the respective positions of clusters and individuals in a
+reduced number of dimensions. In a few simulated cases, the resulting
+clustering of the populations matched exactly the underlying genetic
+structure, even in complex cases with isolation by distance, or when
+there was a hierarchical structure of the clusters, which is difficult
+to recover by other multivariate analyses (see e.g. {1}).
+<br>
+<br>
+Among a growing number of new multivariate techniques {1}, DAPC seems
+to be a very simple, robust, and useful tool for the finding and the
+visualization of clusters of individuals. When such clusters make
+little sense, like in admixture analysis for instance, a simple PC
+analysis may seem more appropriate {2}. While being a model-free
+approach, DAPC efficiency in recovering true genetic structure may be
+due to the fact that principal components are actually related to
+demographic parameters via coalescence times {3}, making the
+distinction between model-based and model-free approaches more subtle
+than previously anticipated. </p>
+<p class="references"><span style="text-decoration: underline;">References:
+</span><br>
+{1} Engelhardt and Stephens, PLoS Genet 2010, 6:e1001117 [<a
+ href="http://www.ncbi.nlm.nih.gov/sites/entrez/20862358?dopt=Abstract&holding=f1000,f1000m,isrctn">PMID:20862358</a>].
+<br>
+{2} Bryc et al. Proc Natl Acad Sci U S A 2010, 107(2):786-91 [<a
+ href="http://www.ncbi.nlm.nih.gov/sites/entrez/20080753?dopt=Abstract&holding=f1000,f1000m,isrctn">PMID:20080753</a>].
+<br>
+{3} McVean G. PLoS Genet 2009, 5:e1000686 [<a
+ href="http://www.ncbi.nlm.nih.gov/sites/entrez/19834557?dopt=Abstract&holding=f1000,f1000m,isrctn">PMID:19834557</a>].</p>
+<div class="competingInterests"> Competing interests: None declared <br>
+<br>
+<br>
+<span style="text-decoration: underline;">To cite this evaluation</span></div>
+<div
+ class="citeEvaluation f1000Expander ui-tabs ui-widget ui-widget-content ui-corner-all ui-tabs-collapsible">
+<div
+ class="citeEvaluationContent ui-tabs-panel ui-widget-content ui-corner-bottom"
+ id="citeEvaluationContent-7142055">
+<p> Excoffier L: "This paper elegantly combines a series of existing
+multivariate methods to detect the genetic structure..." Evaluation of:
+[Jombart T et al. Discriminant analysis of principal components: a new
+method for the analysis of genetically structured populations. <span
+ class="journalname">BMC Genet.</span> <span class="pubdate">2010</span>;
+
+<span class="volume">11</span>:<span class="fpage">94</span>; doi:
+10.1186/1471-2156-11-94]. Faculty of 1000, 14 Dec 2010.
+F1000.com/6949956 </p>
+<p> Short form<br>
+Excoffier L: 2010. F1000.com/6949956 </p>
+</div>
+</div>
+</div>
+</body>
+</html>
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