[adegenet-commits] r289 - in pkg: . R data man misc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 1 20:39:46 CEST 2009
Author: jombart
Date: 2009-04-01 20:39:46 +0200 (Wed, 01 Apr 2009)
New Revision: 289
Added:
pkg/misc/capreo.RData
Removed:
pkg/data/capreo.RData
Modified:
pkg/ChangeLog
pkg/DESCRIPTION
pkg/R/spca.R
pkg/TODO
pkg/man/accessors.Rd
pkg/man/adegenet.package.Rd
pkg/man/selpopsize.Rd
Log:
Updated some files.
Moved capreo (wait for a decent doc).
Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog 2009-04-01 17:27:31 UTC (rev 288)
+++ pkg/ChangeLog 2009-04-01 18:39:46 UTC (rev 289)
@@ -1,3 +1,41 @@
+ CHANGES IN ADEGENET VERSION 1.2-3
+
+
+NEW FEATURES
+
+ o implement handling of presence/absence markers. genind and
+ genpop object now have a 'type' attribute to differentiate between
+ codominant markers (e.g. microsatellite), which is the default
+ type, and presence/absence data (e.g. AFLP). Functions in adegenet
+ now behave according to the type of markers being used.
+
+ o SNP can now be obtained from sequence data, stored as DNAbin
+ (see E. Paradis's package 'ape'). They can be selected to verify
+ any given degree of polymorphism.
+
+ o 'hybridize' can now be used for genotypes having any even degree
+ of ploidy (e.g. tetraploid genotypes).
+
+ o the new function 'pop' can be used to retrieve and set the pop
+ slot of genind object.
+
+ o the new function 'selPopSize' allows one to select a subset of
+ genotypes belonging to well-sampled populations, as defined by a
+ threshold sample size.
+
+ o the new accessor 'locNames' can be used to retrieve real labels
+ of markers and/or alleles.
+
+ o the loadingplot has been modified to allow specifying x axis, so
+ that scoring SNPs along their sequence is now possible.
+
+
+BUG FIXES
+
+ o no bug to fix this version!
+
+
+
CHANGES IN ADEGENET VERSION 1.2-2
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2009-04-01 17:27:31 UTC (rev 288)
+++ pkg/DESCRIPTION 2009-04-01 18:39:46 UTC (rev 289)
@@ -1,6 +1,6 @@
Package: adegenet
Version: 1.2-3
-Date: 2008/07/30
+Date: 2009/04/01
Title: adegenet: a R package for the multivariate analysis of genetic markers.
Author: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>, with contributions from Peter Solymos
Maintainer: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>
Modified: pkg/R/spca.R
===================================================================
--- pkg/R/spca.R 2009-04-01 17:27:31 UTC (rev 288)
+++ pkg/R/spca.R 2009-04-01 18:39:46 UTC (rev 289)
@@ -24,7 +24,7 @@
## first checks
if(!any(inherits(obj,c("genind","genpop")))) stop("obj must be a genind or genpop object.")
invisible(validObject(obj))
- checkType(obj)
+ ## checkType(obj)
if(!require(ade4, quiet=TRUE)) stop("ade4 library is required.")
if(!require(spdep, quiet=TRUE)) stop("spdep library is required.")
Modified: pkg/TODO
===================================================================
--- pkg/TODO 2009-04-01 17:27:31 UTC (rev 288)
+++ pkg/TODO 2009-04-01 18:39:46 UTC (rev 289)
@@ -40,7 +40,7 @@
# NEW IMPLEMENTATIONS:
=====================
-*o* implement handling of presence/absence data -- mostly done, but mostly issues a (fair) error (TJ)
+o implement handling of presence/absence data -- done (TJ)
o add a type argument to genind/genpop objects -- done (TJ)
o make all the required subsequent changes in the package: -- all done, some checks cannot harm (TJ)
- class definition and checks
@@ -59,14 +59,14 @@
- propTyped
- hybridize
- repool
-o select genotypes by population sample size -- done <selpopsize> (TJ)
+o select genotypes by population sample size -- done <selPopSize> (TJ)
o import SNPs from sequence data -- done <DNAbin2genind> (TJ)
# TESTING:
==========
-* test reading from url files.
-* MANDATORY: run some decent testing of AFLP data management:
+o test reading from url files.
+o MANDATORY: run some decent testing of AFLP data management: -- done
- df2genind
- genind
- genind2genpop
@@ -85,7 +85,7 @@
* check all examples and look for possible improvements
* Implement a method to merge different markers for the same individuals
*o* Build accessors for:
-- marker names
+- marker names -- done <locNames> (TJ)
- indiv names
- pop names/factor -- done <pop> (TJ)
- spatial coords
@@ -93,7 +93,7 @@
* Return a spatial object from monmonier (class sp?)
* implement classical Fst sensu Weir 1996 ? Or wait for EP to do it...
* Implement different levels of ploidy in:
-- hybridize
+- hybridize - done (TJ)
- read.structure
- propShared
Deleted: pkg/data/capreo.RData
===================================================================
(Binary files differ)
Modified: pkg/man/accessors.Rd
===================================================================
--- pkg/man/accessors.Rd 2009-04-01 17:27:31 UTC (rev 288)
+++ pkg/man/accessors.Rd 2009-04-01 18:39:46 UTC (rev 289)
@@ -14,6 +14,9 @@
\alias{pop<-}
\alias{pop,genind-method}
\alias{pop<-,genind-method}
+\alias{locNames}
+\alias{locNames,genind-method}
+\alias{locNames,genpop-method}
\title{ Accessors for adegenet objects}
\description{
An accessor is a function that allows to interact with slots of an
@@ -49,9 +52,24 @@
\item{pop}{returns the population factor of the object, using true
(as opposed to generic) levels.}
\item{pop<-}{replacement method for the \code{@pop} slot of an
- object. The content of \code{@pop} and \code{@pop.names} is updated automatically.}
+ object. The content of \code{@pop} and \code{@pop.names} is updated
+ automatically.}
+ \item{locNames}{returns the true names of markers and/or alleles.}
}
}
+\usage{
+nLoc(x, \dots)
+pop(x)
+locNames(x)
+\S4method{locNames}{genind,genpop}(x, withAlleles=FALSE, \dots)
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} or a \linkS4class{genpop} object.}
+ \item{withAlleles}{a logical indicating whether the result should be
+ of the form [locus name].[allele name], instead of [locus name].}
+ \item{\dots}{further arguments to be passed to other methods
+ (currently not used).}
+}
\value{
A \linkS4class{genind} or \linkS4class{genpop} object.
}
@@ -122,5 +140,9 @@
obj$pop.names
pop(obj)
+# illustrate locNames
+locNames(obj)
+locNames(obj, withAlleles=TRUE)
+
}
\keyword{manip}
\ No newline at end of file
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2009-04-01 17:27:31 UTC (rev 288)
+++ pkg/man/adegenet.package.Rd 2009-04-01 18:39:46 UTC (rev 289)
@@ -6,7 +6,9 @@
\title{The adegenet package}
\description{This package is devoted to the multivariate analysis of
- molecular markers data. It defines two formal (S4) classes:
+ genetic markers data. These data can be codominant markers (e.g. microsatellites) or
+ presence/absence data (e.g. AFLP), and have any level of ploidy.
+ 'adegenet' defines two formal (S4) classes:\cr
- \linkS4class{genind}: a class for data of individuals ("genind" stands for genotypes-individuals).\cr
- \linkS4class{genpop}: a class for data of groups of individuals ("genpop" stands for genotypes-populations)\cr
For more information about these classes, type "class ? genind" or
@@ -66,6 +68,11 @@
a \linkS4class{genpop} object.\cr
- \code{\link{repool}} merges genoptypes from different
genetic pools into one single \linkS4class{genind} object.\cr
+ - \code{\link{propTyped}} returns the proportion of available (typed)
+ data, by individual, population, and/or locus.\cr
+ - \code{\link{selPopSize}} subsets data, retaining only genotypes
+ from a population whose sample size is above a given level.\cr
+ - \code{\link{pop}} sets the population of a set of genotypes.\cr
=== ANALYZING DATA ===\cr
@@ -107,8 +114,8 @@
\tabular{ll}{
Package: \tab adegenet\cr
Type: \tab Package\cr
- Version: \tab 1.2-2\cr
- Date: \tab 2008-07-30 \cr
+ Version: \tab 1.2-3\cr
+ Date: \tab 2009-04-01 \cr
License: \tab GPL (>=2)
}
}
Modified: pkg/man/selpopsize.Rd
===================================================================
--- pkg/man/selpopsize.Rd 2009-04-01 17:27:31 UTC (rev 288)
+++ pkg/man/selpopsize.Rd 2009-04-01 18:39:46 UTC (rev 289)
@@ -1,18 +1,18 @@
\encoding{UTF-8}
\docType{methods}
-\name{selpopsize}
-\alias{selpopsize}
-\alias{selpopsize-methods}
-\alias{selpopsize,ANY-method}
-\alias{selpopsize,genind-method}
+\name{selPopSize}
+\alias{selPopSize}
+\alias{selPopSize-methods}
+\alias{selPopSize,ANY-method}
+\alias{selPopSize,genind-method}
\title{ Select genotypes of well-represented populations}
\description{
- The function \code{selpopsize} checks the sample size of each population in
+ The function \code{selPopSize} checks the sample size of each population in
a \linkS4class{genind} object and keeps only genotypes of populations
having a given minimum size.
}
\usage{
-\S4method{selpopsize}{genind}(x,pop=NULL,nMin=10)
+\S4method{selPopSize}{genind}(x,pop=NULL,nMin=10)
}
\arguments{
\item{x}{a \linkS4class{genind} object}
@@ -31,7 +31,7 @@
data(microbov)
table(pop(microbov))
-obj <- selpopsize(microbov, n=50)
+obj <- selPopSize(microbov, n=50)
obj
table(pop(obj))
Added: pkg/misc/capreo.RData
===================================================================
(Binary files differ)
Property changes on: pkg/misc/capreo.RData
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
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