[Genabel-commits] r1182 - pkg/GenABEL/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 4 10:53:28 CEST 2013
Author: yurii
Date: 2013-04-04 10:53:28 +0200 (Thu, 04 Apr 2013)
New Revision: 1182
Modified:
pkg/GenABEL/man/egscore.Rd
pkg/GenABEL/man/export.plink.Rd
pkg/GenABEL/man/ibs.Rd
pkg/GenABEL/man/qtscore.Rd
Log:
accumulated changes in Rd
Modified: pkg/GenABEL/man/egscore.Rd
===================================================================
--- pkg/GenABEL/man/egscore.Rd 2013-04-04 08:48:56 UTC (rev 1181)
+++ pkg/GenABEL/man/egscore.Rd 2013-04-04 08:53:28 UTC (rev 1182)
@@ -1,84 +1,89 @@
\name{egscore}
\alias{egscore}
\title{Fast score test for association, corrected with PC}
-\description{
-Fast score test for association between a trait and genetic polymorphism,
-adjusted for possible stratification by principal components.
-}
\usage{
-egscore(formula,data,snpsubset,idsubset,kinship.matrix,naxes=3,strata,times=1,quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0)
+ egscore(formula, data, snpsubset, idsubset,
+ kinship.matrix, naxes = 3, strata, times = 1,
+ quiet = FALSE, bcast = 10, clambda = TRUE, propPs = 1)
}
\arguments{
- \item{formula}{Formula describing fixed effects to be used in analysis, e.g.
- y ~ a + b means that outcome (y) depends on two covariates, a and b.
- If no covariates used in analysis, skip the right-hand side of the
- equation.
- }
+ \item{formula}{Formula describing fixed effects to be
+ used in analysis, e.g. y ~ a + b means that outcome (y)
+ depends on two covariates, a and b. If no covariates
+ used in analysis, skip the right-hand side of the
+ equation.}
+
\item{data}{An object of \code{\link{gwaa.data-class}}}
- \item{snpsubset}{Index, character or logical vector with subset of SNPs to run analysis on.
- If missing, all SNPs from \code{data} are used for analysis.}
- \item{idsubset}{Index, character or logical vector with subset of IDs to run analysis on.
- If missing, all people from \code{data/cc} are used for analysis.}
- \item{kinship.matrix}{kinship matrix, as returned by \code{\link{ibs}},
- Use weight="freq" with \code{\link{ibs}} and do not forget to repalce
- the diagonal with Var returned by \code{\link{hom}}, as shown in example!}
- \item{naxes}{Number of axes of variation to be used in adjustment (should be much smaller
- than number of subjects)}
- \item{strata}{Stratification variable. If provieded, scores are computed within strata and
- then added up.}
- \item{times}{If more then one, the number of replicas to be used in derivation of
- empirical genome-wide significance.
- }
+
+ \item{snpsubset}{Index, character or logical vector with
+ subset of SNPs to run analysis on. If missing, all SNPs
+ from \code{data} are used for analysis.}
+
+ \item{idsubset}{Index, character or logical vector with
+ subset of IDs to run analysis on. If missing, all people
+ from \code{data/cc} are used for analysis.}
+
+ \item{kinship.matrix}{kinship matrix, as returned by
+ \code{\link{ibs}}, Use weight="freq" with
+ \code{\link{ibs}} and do not forget to repalce the
+ diagonal with Var returned by \code{\link{hom}}, as shown
+ in example!}
+
+ \item{naxes}{Number of axes of variation to be used in
+ adjustment (should be much smaller than number of
+ subjects)}
+
+ \item{strata}{Stratification variable. If provieded,
+ scores are computed within strata and then added up.}
+
+ \item{times}{If more then one, the number of replicas to
+ be used in derivation of empirical genome-wide
+ significance.}
+
\item{quiet}{do not print warning messages}
- \item{bcast}{If the argument times > 1, progress is reported once in bcast replicas}
- \item{clambda}{If inflation facot Lambda is estimated as lower then one, this parameter
- controls if the original P1df (clambda=TRUE) to be reported in Pc1df,
- or the original 1df statistics is to be multiplied onto this "deflation"
- factor (clambda=FALSE).
- If a numeric value is provided, it is used as a correction factor.}
- \item{propPs}{proportion of non-corrected P-values used to estimate the inflation factor Lambda,
- passed directly to the \code{\link{estlambda}}}
-}
-\details{
-The idea of this test is to use genomic kinship matrix to first,
-derive axes of genetic variation (principal components), and, second,
-adjust both trait and genotypes onto these axes. Note that
-the diagonal of the kinship matrix should be replaced
-(default it is .5+F, and for EIGENSTRAT one needs variance).
-These variances are porduced by \code{\link{hom}} function (see
-example).
-The traits is first analysed using LM and with covariates as specified with
-formula and also with axes of variation as predictors. Corrected genotypes are
-defined as residuals from regression of genotypes onto axes (which are
-orthogonal). Correlaton between corrected genotypes and phenotype is computed,
-and test statistics is defined as square of this correlation times
-(N - K - 1), where N is number of genotyped subjects and K is the number of
-axes.
+ \item{bcast}{If the argument times > 1, progress is
+ reported once in bcast replicas}
-This test is defined only for 1 d.f.
+ \item{clambda}{If inflation facot Lambda is estimated as
+ lower then one, this parameter controls if the original
+ P1df (clambda=TRUE) to be reported in Pc1df, or the
+ original 1df statistics is to be multiplied onto this
+ "deflation" factor (clambda=FALSE). If a numeric value
+ is provided, it is used as a correction factor.}
+
+ \item{propPs}{proportion of non-corrected P-values used
+ to estimate the inflation factor Lambda, passed directly
+ to the \code{\link{estlambda}}}
}
-%% \note{
-%% Original method of Price et al. uses covariance for both diagonal and off-diagonal
-%% elements of the matrix on which PC are computed. Kinship matrix returned by GenABEL
-%% contains 0.5+F (!= covariance) on the diagonal. As a temporary solution we now
-%% replace diagonal elements with 0.5
-%% }
\value{
Object of class \code{\link{scan.gwaa-class}}
}
-\references{
- Price A. L. et al, Principal components analysis corrects for
- stratification in genome-wide association studies. Nat Genet
- 38: 904-909.
+\description{
+ Fast score test for association between a trait and
+ genetic polymorphism, adjusted for possible
+ stratification by principal components.
}
-\author{Yurii Aulchenko}
-%\note{}
-\seealso{
-\code{\link{qtscore}},
-\code{\link{mmscore}},
-\code{\link{ibs}},
-\code{\link{scan.gwaa-class}}
+\details{
+ The idea of this test is to use genomic kinship matrix to
+ first, derive axes of genetic variation (principal
+ components), and, second, adjust both trait and genotypes
+ onto these axes. Note that the diagonal of the kinship
+ matrix should be replaced (default it is .5+F, and for
+ EIGENSTRAT one needs variance). These variances are
+ porduced by \code{\link{hom}} function (see example).
+
+ The traits is first analysed using LM and with covariates
+ as specified with formula and also with axes of variation
+ as predictors. Corrected genotypes are defined as
+ residuals from regression of genotypes onto axes (which
+ are orthogonal). Correlaton between corrected genotypes
+ and phenotype is computed, and test statistics is defined
+ as square of this correlation times (N - K - 1), where N
+ is number of genotyped subjects and K is the number of
+ axes.
+
+ This test is defined only for 1 d.f.
}
\examples{
data(ge03d2c)
@@ -89,4 +94,17 @@
a <- egscore(dm2~sex+age,data=ge03d2c,kin=gkin)
plot(a,df="Pc1df")
}
-\keyword{htest}% at least one, from doc/KEYWORDS
+\author{
+ Yurii Aulchenko
+}
+\references{
+ Price A. L. et al, Principal components analysis corrects
+ for stratification in genome-wide association studies.
+ Nat Genet 38: 904-909.
+}
+\seealso{
+ \code{\link{qtscore}}, \code{\link{mmscore}},
+ \code{\link{ibs}}, \code{\link{scan.gwaa-class}}
+}
+\keyword{htest}
+
Modified: pkg/GenABEL/man/export.plink.Rd
===================================================================
--- pkg/GenABEL/man/export.plink.Rd 2013-04-04 08:48:56 UTC (rev 1181)
+++ pkg/GenABEL/man/export.plink.Rd 2013-04-04 08:53:28 UTC (rev 1182)
@@ -3,7 +3,7 @@
\title{Export GenABEL data in PLINK format}
\usage{
export.plink(data, filebasename = "plink",
- phenotypes = "all", transpose = FALSE,
+ phenotypes = "all", transpose = TRUE,
export012na = FALSE, ...)
}
\arguments{
Modified: pkg/GenABEL/man/ibs.Rd
===================================================================
--- pkg/GenABEL/man/ibs.Rd 2013-04-04 08:48:56 UTC (rev 1181)
+++ pkg/GenABEL/man/ibs.Rd 2013-04-04 08:53:28 UTC (rev 1182)
@@ -71,7 +71,7 @@
}
\examples{
data(ge03d2c)
-set.seed(1)
+set.seed(7)
# compute IBS based on a random sample of 1000 autosomal marker
selectedSnps <- sample(autosomal(ge03d2c),1000,replace=FALSE)
a <- ibs(ge03d2c,snps=selectedSnps)
Modified: pkg/GenABEL/man/qtscore.Rd
===================================================================
--- pkg/GenABEL/man/qtscore.Rd 2013-04-04 08:48:56 UTC (rev 1181)
+++ pkg/GenABEL/man/qtscore.Rd 2013-04-04 08:53:28 UTC (rev 1182)
@@ -28,7 +28,7 @@
\item{trait.type}{"gaussian" or "binomial" or "guess"
(later option guesses trait type)}
- \item{times}{If more then one, the number of replicas to
+ \item{times}{If more than one, the number of replicas to
be used in derivation of empirical genome-wide
significance. See \code{\link{emp.qtscore}}, which calls
qtscore with times>1 for details}
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