[adegenet-commits] r845 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Mar 9 14:37:54 CET 2011
Author: jombart
Date: 2011-03-09 14:37:54 +0100 (Wed, 09 Mar 2011)
New Revision: 845
Modified:
pkg/R/SNPbin.R
pkg/man/find.clusters.Rd
pkg/man/genlight.Rd
pkg/man/read.PLINK.Rd
Log:
Added chromosome and position as slots.
Accessors/replacement methods are OK.
find.cluster needs more work to allow dudi arg in all methods;
need for a find.cluster for genlight objects.
Modified: pkg/R/SNPbin.R
===================================================================
--- pkg/R/SNPbin.R 2011-03-09 10:53:33 UTC (rev 844)
+++ pkg/R/SNPbin.R 2011-03-09 13:37:54 UTC (rev 845)
@@ -668,12 +668,21 @@
## chromosome
+setGeneric("chromosome", function(x, ...) standardGeneric("chromosome"))
+setGeneric("chromosome<-", function(x, value) standardGeneric("chromosome<-"))
+setGeneric("chr", function(x,...) standardGeneric("chr"))
+setGeneric("chr<-", function(x, value) standardGeneric("chr<-"))
+
setMethod("chromosome","genlight", function(x,...){
if(length(x at chromosome)==0) return(NULL)
return(x at chromosome)
})
+setMethod("chr","genlight", function(x,...){
+ return(chromosome(x))
+})
+
setReplaceMethod("chromosome","genlight",function(x,value) {
if(is.null(value)){
slot(x, "chromosome", check=TRUE) <- value
@@ -684,9 +693,17 @@
return(x)
})
+setReplaceMethod("chr","genlight",function(x,value) {
+ chromosome(x) <- value
+ return(x)
+})
+
## position
+setGeneric("position", function(x, ...) standardGeneric("position"))
+setGeneric("position<-", function(x, value) standardGeneric("position<-"))
+
setMethod("position","genlight", function(x,...){
if(length(x at position)==0) return(NULL)
return(x at position)
Modified: pkg/man/find.clusters.Rd
===================================================================
--- pkg/man/find.clusters.Rd 2011-03-09 10:53:33 UTC (rev 844)
+++ pkg/man/find.clusters.Rd 2011-03-09 13:37:54 UTC (rev 845)
@@ -28,7 +28,7 @@
n.clust=NULL, stat=c("BIC","AIC", "WSS"),
choose.n.clust=TRUE,criterion=c("diffNgroup", "min","goesup", "smoothNgoesup", "goodfit"),
max.n.clust=round(nrow(x)/10), n.iter=1e5, n.start=10,
- center=TRUE, scale=TRUE, \ldots)
+ center=TRUE, scale=TRUE, \ldots, dudi=NULL)
\method{find.clusters}{matrix}(x, \ldots)
@@ -99,6 +99,10 @@
\item{\ldots}{further arguments to be passed to other functions. For
\code{find.clusters.matrix}, arguments are to match those of the
\code{data.frame} method.}
+ \item{dudi}{optionally, a multivariate analysis with the class
+ \code{dudi} (from the ade4 package). If provided, prior PCA will be
+ ignored, and this object will be used as a prior step for variable
+ orthogonalisation.}
}
\details{
=== ON THE SELECTION OF K ===\cr
Modified: pkg/man/genlight.Rd
===================================================================
--- pkg/man/genlight.Rd 2011-03-09 10:53:33 UTC (rev 844)
+++ pkg/man/genlight.Rd 2011-03-09 13:37:54 UTC (rev 845)
@@ -19,6 +19,18 @@
\alias{indNames<-,genlight-method}
\alias{alleles,genlight-method}
\alias{alleles<-,genlight-method}
+\alias{chromosome}
+\alias{chromosome<-}
+\alias{chromosome,genlight-method}
+\alias{chromosome<-,genlight-method}
+\alias{chr}
+\alias{chr<-}
+\alias{chr,genlight-method}
+\alias{chr<-,genlight-method}
+\alias{position}
+\alias{position<-}
+\alias{position,genlight-method}
+\alias{position<-,genlight-method}
\alias{pop,genlight-method}
\alias{pop<-,genlight-method}
\alias{NA.posi}
@@ -78,8 +90,14 @@
\item{\code{loc.names}}{an optional vector of characters giving the labels
of the SNPs.}
\item{\code{loc.all}}{an optional vector of characters indicating
- the alleles of each SNP; for each SNP, alleles must be coded by two
- letters separated by '/', e.g. 'a/t' is valid, but 'a t' or 'a |t' are not.}
+ the alleles of each SNP; for each SNP, alleles must be coded by two
+ letters separated by '/', e.g. 'a/t' is valid, but 'a t' or 'a |t'
+ are not.}
+ \item{\code{chromosome}}{an optional factor indicating the
+ chromosome to which each SNP belongs.}
+ \item{\code{position}}{an optional vector of integers indicating the
+ position of the SNPs.}
+ \item{\code{other}}{an optional list storing miscellaneous information.}
}
}
\section{Slots}{
@@ -118,28 +136,37 @@
supported arguments.}
\item{show}{\code{signature(x = "genlight")}: printing of the
object.}
+
\item{$}{\code{signature(x = "genlight")}: similar to the @ operator;
used to access the content of slots of the object.}
\item{$<-}{\code{signature(x = "genlight")}: similar to the @ operator;
used to replace the content of slots of the object.}
+
\item{nInd}{\code{signature(x = "genlight")}: returns the number of
individuals in the object.}
\item{nLoc}{\code{signature(x = "genlight")}: returns the number of
SNPs in the object.}
+
\item{names}{\code{signature(x = "genlight")}: returns the names of
the slots of the object.}
- \item{ploidy}{\code{signature(x = "genlight")}: returns the ploidy of
- the genotypes.}
- \item{NA.posi}{\code{signature(x = "genlight")}: returns the indices
- of missing values (NAs) as a list with one vector of integer for each individual.}
+
\item{indNames}{\code{signature(x = "genlight")}: returns the names of
the individuals, if provided when the object was contructed.}
\item{indNames<-}{\code{signature(x = "genlight")}: sets the names of
- the individuals using a character vector of length \code{nInd(x)}.}
+ the individuals using a character vector of length
+ \code{nInd(x)}.}
+
\item{locNames}{\code{signature(x = "genlight")}: returns the names of
the loci, if provided when the object was contructed.}
\item{locNames<-}{\code{signature(x = "genlight")}: sets the names of
the SNPs using a character vector of length \code{nLoc(x)}.}
+
+ \item{ploidy}{\code{signature(x = "genlight")}: returns the ploidy of
+ the genotypes.}
+
+ \item{NA.posi}{\code{signature(x = "genlight")}: returns the indices
+ of missing values (NAs) as a list with one vector of integer for each individual.}
+
\item{alleles}{\code{signature(x = "genlight")}: returns the names
of the alleles of each SNPs, if provided when the object was
contructed.}
@@ -147,15 +174,36 @@
of the alleles of each SNPs using a character vector of length
\code{nLoc(x)}; for each SNP, two alleles must be provided,
separated by a "/", e.g. 'a/t', 'c/a', etc.}
+
+ \item{chromosome}{\code{signature(x = "genlight")}: returns a factor
+ indicating the chromosome of each SNPs, or NULL if the information
+ is missing.}
+ \item{chromosome<-}{\code{signature(x = "genlight")}: sets the
+ chromosome to which SNPs belong using a factor of length
+ \code{nLoc(x)}.}
+
+ \item{chr}{\code{signature(x = "genlight")}: shortcut for
+ \code{chromosome}.}
+ \item{chr<-}{\code{signature(x = "genlight")}: shortcut for
+ \code{chromosome<-}.}
+
+ \item{position}{\code{signature(x = "genlight")}: returns an integer
+ vector indicating the position of each SNPs, or NULL if the
+ information is missing.}
+ \item{position<-}{\code{signature(x = "genlight")}: sets the
+ positions of the SNPs using an integer vector of length
+ \code{nLoc(x)}.}
+
\item{pop}{\code{signature(x = "genlight")}: returns a factor
indicating the population of each individual, if provided when the
object was contructed.}
\item{pop<-}{\code{signature(x = "genlight")}: sets the population
of each individual using a factor of length \code{nInd(x)}.}
- \item{pop}{\code{signature(x = "genlight")}: returns the content of
+ \item{other}{\code{signature(x = "genlight")}: returns the content of
the slot \code{@other}.}
- \item{pop<-}{\code{signature(x = "genlight")}: sets the content of
+ \item{other<-}{\code{signature(x = "genlight")}: sets the content of
the slot \code{@other}.}
+
\item{as.matrix}{\code{signature(x = "genlight")}: converts a
\code{genlight} object into a matrix of integers, with individuals
in rows and SNPs in columns. The S4 method 'as' can be used as
@@ -165,6 +213,7 @@
\code{genlight} object into a list of genotypes coded as vector of
integers (numbers of second allele). The S4 method 'as' can be
used as well (e.g. as(x, "list")).}
+
\item{cbind}{\code{signature(x = "genlight")}: merges several
\linkS4class{genlight} objects by column, i.e. regroups data of
identical individuals genotyped for different SNPs.}
Modified: pkg/man/read.PLINK.Rd
===================================================================
--- pkg/man/read.PLINK.Rd 2011-03-09 10:53:33 UTC (rev 844)
+++ pkg/man/read.PLINK.Rd 2011-03-09 13:37:54 UTC (rev 845)
@@ -104,7 +104,7 @@
\code{snpMatrix}.
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
-\examples{
+% \examples{
-}
+% }
\keyword{manip}
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