[adegenet-commits] r133 - in pkg: R data man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 25 19:22:38 CEST 2008
Author: jombart
Date: 2008-06-25 19:22:38 +0200 (Wed, 25 Jun 2008)
New Revision: 133
Added:
pkg/data/microbov.RData
pkg/data/nancycats.RData
pkg/data/sim2pop.RData
pkg/data/spcaIllus.RData
pkg/man/scale.Rd
Removed:
pkg/data/microbov.rda
pkg/data/nancycats.rda
pkg/data/sim2pop.rda
pkg/data/spcaIllus.rda
Modified:
pkg/R/scale.R
pkg/man/as.genind.Rd
pkg/man/genind.Rd
Log:
Added the @ploidy slot in genind.
Added documentation for scaleGen
Modified: pkg/R/scale.R
===================================================================
--- pkg/R/scale.R 2008-06-25 16:36:11 UTC (rev 132)
+++ pkg/R/scale.R 2008-06-25 17:22:38 UTC (rev 133)
@@ -4,9 +4,15 @@
setGeneric("scaleGen", function(x,...){standardGeneric("scaleGen")})
setMethod("scaleGen", "genind", function(x, center=TRUE, scale=TRUE,
- method=c("sigma", "binom"), truenames=TRUE){
+ method=c("sigma", "binom"), missing=c("NA","0","mean"), truenames=TRUE){
method <- match.arg(method)
+ missing <- match.arg(missing)
+
+ ## handle "missing" arg
+ if(missing %in% c("0","mean")){
+ x <- na.replace(x,method=missing)
+ }
## handle specific cases
if(scale & tolower(method)=="binom"){
@@ -36,10 +42,11 @@
setMethod("scaleGen", "genpop", function(x, center=TRUE, scale=TRUE,
- method=c("sigma", "binom"), missing=NA, truenames=TRUE){
+ method=c("sigma", "binom"), missing=c("NA","0","mean"), truenames=TRUE){
method <- match.arg(method)
-
+ missing <- match.arg(missing)
+
## make allele frequencies here
X <- makefreq(x,quiet=TRUE,missing=missing,truenames=truenames)$tab
Added: pkg/data/microbov.RData
===================================================================
(Binary files differ)
Property changes on: pkg/data/microbov.RData
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: pkg/data/microbov.rda
===================================================================
(Binary files differ)
Added: pkg/data/nancycats.RData
===================================================================
(Binary files differ)
Property changes on: pkg/data/nancycats.RData
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: pkg/data/nancycats.rda
===================================================================
(Binary files differ)
Added: pkg/data/sim2pop.RData
===================================================================
(Binary files differ)
Property changes on: pkg/data/sim2pop.RData
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: pkg/data/sim2pop.rda
===================================================================
(Binary files differ)
Added: pkg/data/spcaIllus.RData
===================================================================
(Binary files differ)
Property changes on: pkg/data/spcaIllus.RData
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: pkg/data/spcaIllus.rda
===================================================================
(Binary files differ)
Modified: pkg/man/as.genind.Rd
===================================================================
--- pkg/man/as.genind.Rd 2008-06-25 16:36:11 UTC (rev 132)
+++ pkg/man/as.genind.Rd 2008-06-25 17:22:38 UTC (rev 133)
@@ -20,8 +20,8 @@
}
\usage{
-genind(tab,pop=NULL,prevcall=NULL)
-as.genind(tab,pop=NULL,prevcall=NULL)
+genind(tab,pop=NULL,prevcall=NULL, ploidy=2)
+as.genind(tab,pop=NULL,prevcall=NULL, ploidy=2)
is.genind(x)
}
@@ -30,6 +30,8 @@
allelic frequencies, i.e. like in a genind object}
\item{pop}{a factor giving the population of each genotype in 'x'}
\item{prevcall}{call of an object}
+ \item{ploidy}{an integer indicating the degree of ploidy of
+ the genotypes. Beware: 2 is not an integer, but as.integer(2) is.}
\item{x}{an object}
}
\value{
Modified: pkg/man/genind.Rd
===================================================================
--- pkg/man/genind.Rd 2008-06-25 16:36:11 UTC (rev 132)
+++ pkg/man/genind.Rd 2008-06-25 17:22:38 UTC (rev 133)
@@ -16,22 +16,24 @@
of \$.
}
\section{Slots}{
- \describe{
+ \describe{
\item{\code{tab}:}{matrix of genotypes -in rows- for all alleles -in
- columns-. Values are frequency: '0' if the genotype does not have
- the corresponding allele, '1' for an homozygote and 0.5 for an
- heterozygte.Rows and columns are given generic names.}
+ columns-. Values are frequency: '0' if the genotype does not have
+ the corresponding allele, '1' for an homozygote and 0.5 for an
+ heterozygte.Rows and columns are given generic names.}
\item{\code{loc.names}:}{character vector containing the real names of the loci}
\item{\code{loc.fac}:}{locus factor for the columns of \code{tab}}
\item{\code{loc.nall}:}{integer vector giving the number of alleles per locus}
\item{\code{all.names}:}{list having one component per locus, each containing a character vector of alleles names}
\item{\code{call}:}{the matched call}
\item{\code{ind.names}:}{character vector containing the real names of the
- individuals. Note that as Fstat does not store these names, objects
- converted from .dat files will contain empty \code{ind.names}.}
+ individuals. Note that as Fstat does not store these names, objects
+ converted from .dat files will contain empty \code{ind.names}.}
+ \item{\code{ploidy}:}{ an integer indicating the degree of ploidy of
+ the genotypes. Beware: 2 is not an integer, but as.integer(2) is.}
\item{\code{pop}:}{(optional) factor giving the population of each individual}
\item{\code{pop.names}:}{(optional) vector giving the real names of the
- populations}
+ populations}
\item{\code{other}:}{(optional) a list containing other information}
}
}
Added: pkg/man/scale.Rd
===================================================================
--- pkg/man/scale.Rd (rev 0)
+++ pkg/man/scale.Rd 2008-06-25 17:22:38 UTC (rev 133)
@@ -0,0 +1,53 @@
+\name{scaleGen-methods}
+\docType{methods}
+\alias{scaleGen}
+\alias{scaleGen-methods}
+\alias{scaleGen,genind-method}
+\alias{scaleGen,genpop-method}
+\title{ Compute scaled allele frequencies }
+\description{
+ The generic function \code{scaleGen} is an analogue to the
+ \code{scale} function, but is designed with further arguments giving
+ scaling options.\cr
+
+ Methods are defined for \linkS4class{genind} and \linkS4class{genpop}
+ objects.
+ Both return data.frames of scaled allele frequencies.
+}
+\usage{
+\S4method{scaleGen}{genind}(x, center=TRUE, scale=TRUE, method=c("sigma", "binom"), missing=c("NA","0","mean"),truenames=TRUE)
+\S4method{scaleGen}{genpop}(x, center=TRUE, scale=TRUE, method=c("sigma", "binom"), missing=c("NA","0","mean"),truenames=TRUE)
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} and \linkS4class{genpop} object}
+ \item{center}{a logical stating whether alleles frequencies should be
+ centred to mean zero (default to TRUE). Alternatively, a vector of
+ numeric values, one per allele, can be supplied: these values will be
+ substracted from the allele frequencies.}
+ \item{scale}{a logical stating whether alleles frequencies should be
+ scaled (default to TRUE). Alternatively, a vector of
+ numeric values, one per allele, can be supplied: these values will be
+ substracted from the allele frequencies.}
+ \item{method}{a character indicating the method to be used. See details.}
+ \item{truenames}{a logical indicating whether true labels (as opposed
+ to generic labels) should be used to name the output.}
+ \item{missing}{a character giving the treatment for missing values. Can be "NA", "0" or "mean"}
+ }
+ \value{
+ A \linkS4class{genind} and \linkS4class{genpop} object.
+}
+\details{
+ The argument \code{method} is used as follows:\cr
+
+ - \code{sigma}: scaling is made using the usual standard deviation\cr
+
+ - \code{binom}: scaling is made using the theoretical variance of the
+ allele frequency. This can be used to avoid that frequencies close to
+ 0.5 have a stronger variance that those close to 0 or 1.
+}
+\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\examples{
+
+}
+\keyword{methods}
+\keyword{manip}
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