[adegenet-commits] r1115 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 25 12:09:54 CEST 2013
Author: greatsage
Date: 2013-04-25 12:09:54 +0200 (Thu, 25 Apr 2013)
New Revision: 1115
Modified:
pkg/man/adegenet.package.Rd
Log:
\encoding{UTF-8}
\name{adegenet-package}
\alias{adegenet-package}
\alias{adegenet}
\docType{package}
\title{The adegenet package}
\description{
This package is devoted to the multivariate analysis of
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 three 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
- \linkS4class{genlight}: a class for genome-wide SNP data\cr
For more information about these classes, type "class ? genind",
"class ? genpop", or "?genlight".\cr
Essential functionalities of the package are presented througout 4
tutorial vignettes, accessible using \code{vignette("name-below", package="adegenet")}:\cr
- adegenet-basics: introduction to the package.\cr
- adegenet-spca: multivariate analysis of spatial genetic patterns.\cr
- adegenet-dapc: population structure and group assignment using DAPC.\cr
- adegenet-genomics: introduction to the class \linkS4class{genlight}
for the handling and analysis of genome-wide SNP data.\cr
Important functions are also summarized below.\cr
=== IMPORTING DATA ===\cr
= TO GENIND OBJECTS = \cr
\code{adegenet} imports data to \linkS4class{genind} object from the
following softwares:\cr
- STRUCTURE: see \code{\link{read.structure}}\cr
- GENETIX: see \code{\link{read.genetix}}\cr
- FSTAT: see \code{\link{read.fstat}}\cr
- Genepop: see \code{\link{read.genepop}}\cr
To import data from any of these formats, you can also use the general
function \code{\link{import2genind}}.\cr
In addition, it can extract polymorphic sites from nucleotide and
amino-acid alignments:\cr
- DNA files: use \code{\link[ape]{read.dna}} from the ape package,
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}}
can be used for any level of ploidy.\cr
= TO GENLIGHT OBJECTS = \cr
SNP data can be read from the following formats:\cr
- PLINK: see function \code{\link{read.PLINK}}\cr
- .snp (adegenet's own format): see function \code{\link{read.snp}}\cr
SNP can also be extracted from aligned DNA sequences with the fasta
format, using \code{\link{fasta2genlight}}\cr
=== EXPORTING DATA ===\cr
\code{adegenet} exports data from \linkS4class{genind} object to
formats recognized by other R packages:\cr
- the genetics package: see \code{\link{genind2genotype}}\cr
- the hierfstat package: see \code{\link{genind2hierfstat}}\cr
Genotypes can also be recoded from a \linkS4class{genind} object into
a data.frame of character strings, using any separator between
alleles. This covers formats from many softwares like GENETIX or
STRUCTURE. For this, see \code{\link{genind2df}}.\cr
Also note that the \code{pegas} package imports \linkS4class{genind}
objects using the function \code{as.loci}.
=== MANIPULATING DATA ===\cr
Several functions allow one to manipulate \linkS4class{genind} or
\linkS4class{genpop} objects\cr
- \code{\link{genind2genpop}}: convert a \linkS4class{genind} object
to a \linkS4class{genpop} \cr
- \code{\link{seploc}}: creates one object per marker; for
\linkS4class{genlight} objects, creates blocks of SNPs.\cr
- \code{\link{seppop}}: creates one object per population \cr
- \code{\link{na.replace}}: replaces missing data (NA) in an
approriate way \cr
- \code{\link{truenames}}: restores true names of an object
(\linkS4class{genind} and \linkS4class{genpop} use generic labels)
\cr
- x[i,j]: create a new object keeping only genotypes (or populations)
indexed by 'i' and the alleles indexed by 'j'.\cr
- \code{\link{makefreq}}: returns a table of allelic frequencies from
a \linkS4class{genpop} object.\cr
- \code{\link{repool}} merges genoptypes from different
gene 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
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\cr
- \code{\link{dist.genpop}}: computes 5 genetic distances among populations. \cr
- \code{\link{monmonier}}: implementation of the Monmonier algorithm,
used to seek genetic boundaries among individuals or
populations. Optimized boundaries can be obtained using
\code{\link{optimize.monmonier}}. Object of the class
\code{monmonier} can be plotted and printed using the corresponding
methods. \cr
- \code{\link{spca}}: implements Jombart et al. (2008) spatial
Principal Component Analysis \cr
- \code{\link{global.rtest}}: implements Jombart et al. (2008)
test for global spatial structures \cr
- \code{\link{local.rtest}}: implements Jombart et al. (2008)
test for local spatial structures \cr
- \code{\link{propShared}}: computes the proportion of shared
alleles in a set of genotypes (i.e. from a genind object)\cr
- \code{\link{propTyped}}: function to investigate missing data in
several ways \cr
- \code{\link{scaleGen}}: generic method to scale
\linkS4class{genind} or \linkS4class{genpop} before a principal
component analysis \cr
- \code{\link{Hs}}: computes the average expected heterozygosity by
population in a \linkS4class{genpop}. Classically Used as a measure
of genetic diversity.\cr
- \code{\link{find.clusters}} and \code{\link{dapc}}: implement the
Discriminant Analysis of Principal Component (DAPC, Jombart et al.,
2010).\cr
- \code{\link{seqTrack}}: implements the SeqTrack algorithm for
recontructing transmission trees of pathogens (Jombart et al.,
2010) .\cr
\code{\link{glPca}}: implements PCA for \linkS4class{genlight}
objects.\cr
=== GRAPHICS ===\cr
- \code{\link{colorplot}}: plots points with associated values for up
to three variables represented by colors using the RGB system;
useful for spatial mapping of principal components.\cr
- \code{\link{loadingplot}}: plots loadings of variables. Useful for
representing the contribution of alleles to a given principal
component in a multivariate method. \cr
- \code{\link{scatter.dapc}}: scatterplots for DAPC results.\cr
- \code{\link{compoplot}}: plots membership probabilities from a DAPC
object. \cr
=== SIMULATING DATA ===\cr
- \code{\link{hybridize}}: implements hybridization between two populations. \cr
- \code{\link{haploGen}}: simulates genealogies of haplotypes,
storing full genomes. \cr
% - \code{\link{haploPop}}: simulates populations of haplotypes, using
% different population dynamics, storing SNPs (under development). \cr
- \code{\link{glSim}}: simulates simple \linkS4class{genlight} objects.\cr
=== DATASETS ===\cr
- \code{\link{H3N2}}: Seasonal influenza (H3N2) HA segment data. \cr
- \code{\link{dapcIllus}}: Simulated data illustrating the DAPC. \cr
- \code{\link{eHGDP}}: Extended HGDP-CEPH dataset. \cr
- \code{\link{microbov}}: Microsatellites genotypes of 15 cattle breeds. \cr
- \code{\link{nancycats}}: Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France). \cr
- \code{\link{rupica}}: Microsatellites genotypes of 335 chamois
(Rupicapra rupicapra) from the Bauges mountains (France).\cr
- \code{\link{sim2pop}}: Simulated genotypes of two georeferenced populations.\cr
- \code{\link{spcaIllus}}: Simulated data illustrating the sPCA. \cr
For more information, visit the adegenet website by typing
\code{adegenetWeb()}.\cr
To cite adegenet, please use the reference given by
\code{citation("adegenet")} (or see reference below).
}
\details{
\tabular{ll}{
Package: \tab adegenet\cr
Type: \tab Package\cr
Version: \tab 1.3-8\cr
Date: \tab 2013-04-24 \cr
License: \tab GPL (>=2)
}
}
\author{
Thibaut Jombart <t.jombart at imperial.ac.uk>\cr
Developers: Ismail Ahmed <ismail.ahmed at inserm.fr>, Federico Calboli <f.calboli at imperial.ac.uk>,Tobias Erik Reiners, Peter Solymos, Anne Cori\cr
and contributed datasets from: Katayoun Moazami-Goudarzi, Denis Lalo?\195?\171,
Dominique Pontier, Daniel Maillard, Francois Balloux.
}
\references{
Jombart T. (2008) adegenet: a R package for the multivariate analysis
of genetic markers \emph{Bioinformatics} 24: 1403-1405. doi:
10.1093/bioinformatics/btn129\cr
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
principal components: a new method for the analysis of genetically
structured populations. BMC Genetics 11:94.
doi:10.1186/1471-2156-11-94\cr
Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease
outbreaks from genetic data: a graph approach. \emph{Heredity}. doi:
10.1038/hdy.2010.78.\cr
Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. (2008) Revealing
cryptic spatial patterns in genetic variability by a new multivariate
method. \emph{Heredity}, \bold{101}, 92--103.\cr
See adegenet website: \url{http://adegenet.r-forge.r-project.org/}\cr
Please post your questions on 'the adegenet forum': adegenet-forum at lists.r-forge.r-project.org
}
\keyword{manip}
\keyword{multivariate}
\seealso{
adegenet is related to several packages, in particular:\cr
- \code{ade4} for multivariate analysis\cr
- \code{pegas} for population genetics tools\cr
- \code{ape} for phylogenetics and DNA data handling\cr
- \code{seqinr} for handling nucleic and proteic sequences\cr
}
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2013-04-24 18:44:43 UTC (rev 1114)
+++ pkg/man/adegenet.package.Rd 2013-04-25 10:09:54 UTC (rev 1115)
@@ -197,7 +197,7 @@
}
\author{
Thibaut Jombart <t.jombart at imperial.ac.uk>\cr
- Developpers: Ismail Ahmed <ismail.ahmed at inserm.fr>, Federico Calboli <f.calboli at imperial.ac.uk>,Tobias Erik Reiners, Peter Solymos, Anne Cori\cr
+ Developers: Ismail Ahmed <ismail.ahmed at inserm.fr>, Federico Calboli <f.calboli at imperial.ac.uk>,Tobias Erik Reiners, Peter Solymos, Anne Cori\cr
and contributed datasets from: Katayoun Moazami-Goudarzi, Denis Laloë,
Dominique Pontier, Daniel Maillard, Francois Balloux.
}
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