[adegenet-commits] r669 - in pkg: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 22 13:21:00 CEST 2010
Author: jombart
Date: 2010-09-22 13:21:00 +0200 (Wed, 22 Sep 2010)
New Revision: 669
Modified:
pkg/ChangeLog
pkg/DESCRIPTION
pkg/R/sequences.R
pkg/man/adegenet.package.Rd
pkg/man/fstat.Rd
Log:
Stuff for the new release.
Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog 2010-09-16 14:43:31 UTC (rev 668)
+++ pkg/ChangeLog 2010-09-22 11:21:00 UTC (rev 669)
@@ -1,3 +1,20 @@
+ CHANGES IN ADEGENET VERSION 1.2-6
+
+
+NEW FEATURES
+
+ o pairwise.fst: computes Nei's pairwise Fst between populations
+
+ o alignment2genind: extract polymorphism from nucleic and proteic
+ aligned sequences with the 'alignment' format, returning a genind object.
+
+
+BUG FIXES
+
+ o fixed a minor issue in Hs, occuring in fixed loci for a given population.
+
+
+
CHANGES IN ADEGENET VERSION 1.2-5
@@ -323,7 +340,7 @@
implement the Monmonier algorithm. While not restrained to genetic
data analysis, this method can be used to find genetic boundaries
among individuals or populations based on their allelic
- frequencies and spatial coordinates.
+ frequencies and spatial coordinates.
BUG FIXES
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2010-09-16 14:43:31 UTC (rev 668)
+++ pkg/DESCRIPTION 2010-09-22 11:21:00 UTC (rev 669)
@@ -1,13 +1,13 @@
Package: adegenet
Version: 1.2-6
-Date: 2010/07/14
+Date: 2010/09/22
Title: adegenet: a R package for the multivariate analysis of genetic markers.
Author: Thibaut Jombart <t.jombart at imperial.ac.uk>
with contributions of: Peter Solymos, Francois Balloux
and contributed datasets from: Katayoun Moazami-Goudarzi, Denis Laloe,
Dominique Pontier, Daniel Maillard, Francois Balloux
Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>
-Suggests: ade4, genetics, hierfstat, spdep, tripack, ape, pegas, graph, RBGL
+Suggests: ade4, genetics, hierfstat, spdep, tripack, ape, pegas, graph, RBGL, seqinr
Depends: methods, MASS
Description: Classes and functions for genetic data analysis within the multivariate framework.
Collate: classes.R basicMethods.R handling.R auxil.R setAs.R find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R chooseCN.R genind2genpop.R loadingplot.R sequences.R gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R export.R HWE.R propTyped.R zzz.R
Modified: pkg/R/sequences.R
===================================================================
--- pkg/R/sequences.R 2010-09-16 14:43:31 UTC (rev 668)
+++ pkg/R/sequences.R 2010-09-22 11:21:00 UTC (rev 669)
@@ -82,8 +82,8 @@
alignment2genind <- function(x, pop=NULL, exp.char=c("a","t","g","c"), na.char="-", polyThres=1/100){
## misc checks
+ if(!require(seqinr)) stop("The package seqinr is required.")
if(!inherits(x,"alignment")) stop("x is not a alignment object")
- if(!require(seqinr)) stop("The package seqinr is required.")
N <- length(x$seq)
if(!is.null(x$nam) && length(x$nam)!=N) stop("Inconsistent names in x (length of x$nam and x$seq do not match). ")
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2010-09-16 14:43:31 UTC (rev 668)
+++ pkg/man/adegenet.package.Rd 2010-09-22 11:21:00 UTC (rev 669)
@@ -36,6 +36,12 @@
and then extract SNPs from DNA alignments using
\code{\link{DNAbin2genind}}. \cr
+ - protein sequences alignments: polymorphic sites can be extracted from
+ protein sequences alignments in \code{alignment} format (package
+ \code{seqinr}, see \code{\link[seqinr]{as.alignment}}) using the
+ function \code{\link{alignment2genind}}. \cr
+
+
It is also possible to read genotypes coded by character strings from
a data.frame in which genotypes are in rows, markers in columns. For
this, use \code{\link{df2genind}}. Note that \code{\link{df2genind}}
@@ -83,6 +89,7 @@
Several functions allow to use usual, and less usual analyses:\cr
- \code{\link{HWE.test.genind}}: performs HWE test for all
populations and loci combinations \cr
+ - \code{\link{pairwise.fst}}: computes simple pairwise Fst between populations
- \code{\link{gstat.randtest}}: performs a Monte Carlo test of Goudet's G statistic, measuring
population structure (based on \code{\link[hierfstat]{g.stats.glob}} package \code{hierfstat}).\cr
- \code{\link{dist.genpop}}: computes 5 genetic distances among populations. \cr
@@ -159,7 +166,7 @@
Package: \tab adegenet\cr
Type: \tab Package\cr
Version: \tab 1.2-6\cr
- Date: \tab 2010-07-14 \cr
+ Date: \tab 2010-09-22 \cr
License: \tab GPL (>=2)
}
}
@@ -193,5 +200,6 @@
- \code{ade4} for multivariate analysis\cr
- \code{ape} for phylogenetics and DNA data handling\cr
- \code{pegas} for population genetics tools\cr
+ - \code{seqinr} for handling nucleic and proteic sequences\cr
}
Modified: pkg/man/fstat.Rd
===================================================================
--- pkg/man/fstat.Rd 2010-09-16 14:43:31 UTC (rev 668)
+++ pkg/man/fstat.Rd 2010-09-22 11:21:00 UTC (rev 669)
@@ -1,6 +1,9 @@
\encoding{UTF-8}
\name{fstat}
\alias{fstat}
+\alias{Fst}
+\alias{FST}
+\alias{fst}
\alias{pairwise.fst}
\title{F statistics for genind objects}
\description{
@@ -37,6 +40,10 @@
\seealso{\code{\link{Hs}}, \code{\link[hierfstat]{varcomp.glob}},
\code{\link{gstat.randtest}}
}
+\references{
+ Nei, M. (1973) Analysis of gene diversity in subdivided
+ populations. Proc Natl Acad Sci USA, 70: 3321-3323
+}
\details{
Let A and B be two populations of population sizes \eqn{n_A} and
\eqn{n_B}, with expected heterozygosity Hs(A) and Hs(B),
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