[Genabel-commits] r1947 - in pkg/MixABEL: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Apr 27 17:05:11 CEST 2015
Author: lckarssen
Date: 2015-04-27 17:05:11 +0200 (Mon, 27 Apr 2015)
New Revision: 1947
Modified:
pkg/MixABEL/NAMESPACE
pkg/MixABEL/R/MixABEL-package.R
pkg/MixABEL/R/fgls.R
pkg/MixABEL/man/FGLS.Rd
pkg/MixABEL/man/FastMixedModel.Rd
pkg/MixABEL/man/GWFGLS.Rd
pkg/MixABEL/man/MixABEL-package.Rd
pkg/MixABEL/man/summaryFGLS.Rd
Log:
Updated MixABEL Roxygen2 documentation so that it gets correctly generated (including the NAMESPACE file) when running the document() function from the devtools package.
Modified: pkg/MixABEL/NAMESPACE
===================================================================
--- pkg/MixABEL/NAMESPACE 2015-04-27 12:47:56 UTC (rev 1946)
+++ pkg/MixABEL/NAMESPACE 2015-04-27 15:05:11 UTC (rev 1947)
@@ -1,15 +1,11 @@
-useDynLib(MixABEL)
-
-export(
- rwth_caller,
- FastMixedModel,
- GWFGLS,
- FGLS,
- summaryFGLS #,
- #deliver.data
- )
-
-import(DatABEL,
- GenABEL,
- MASS,
- mvtnorm)
+# Generated by roxygen2 (4.1.0): do not edit by hand
+
+export(FGLS)
+export(FastMixedModel)
+export(GWFGLS)
+export(summaryFGLS)
+import(DatABEL)
+import(GenABEL)
+import(MASS)
+import(mvtnorm)
+useDynLib(MixABEL)
Modified: pkg/MixABEL/R/MixABEL-package.R
===================================================================
--- pkg/MixABEL/R/MixABEL-package.R 2015-04-27 12:47:56 UTC (rev 1946)
+++ pkg/MixABEL/R/MixABEL-package.R 2015-04-27 15:05:11 UTC (rev 1947)
@@ -1,10 +1,15 @@
#' MixABEL package
-#'
-#' Package for fast (genome-wide) association analysis
-#' using mixed models. Main functions:
-#' \link{FastMixedModel}, \link{GWFGLS}
-#'
+#'
+#' Package for fast (genome-wide) association analysis
+#' using mixed models. Main functions:
+#' \link{FastMixedModel}, \link{GWFGLS}
+#'
#' @author Yurii Aulchenko, William Astle, Erik Roos, Marcel Kempenaar
-#'
+#'
+#' @docType package
+#' @name MixABEL-package
+#' @aliases "MixABEL"
+#' @useDynLib MixABEL
+#' @import DatABEL GenABEL MASS mvtnorm
-"MixABEL-package" <- function() {}
\ No newline at end of file
+"MixABEL-package" <- function() {}
Modified: pkg/MixABEL/R/fgls.R
===================================================================
--- pkg/MixABEL/R/fgls.R 2015-04-27 12:47:56 UTC (rev 1946)
+++ pkg/MixABEL/R/fgls.R 2015-04-27 15:05:11 UTC (rev 1947)
@@ -19,6 +19,8 @@
#'
#' @author Yurii Aulchenko
#'
+#' @export
+#'
FGLS <- function(Y,X,W=NULL,test="wald",whichtest = c(FALSE,rep(TRUE,dim(X)[2]-1)))
{
# do checks
@@ -133,6 +135,8 @@
#'
#' @author Yurii Aulchenko
#'
+#' @export
+#'
summaryFGLS <- function(x,verbosity=1,varcov=FALSE,include.means=FALSE) {
out <- c(x$n,x$T2,x$df,pchisq(x$T2,df=x$df,lower.tail=FALSE))
names(out) <- c("n","Chisq","df","P-value")
@@ -172,6 +176,8 @@
}
return(out)
}
+
+
#' Genome-wide FGLS
#'
#' Genome-wide Feasible GLS
@@ -260,6 +266,8 @@
#' @author Yurii Aulchenko
#'
#'
+#' @export
+#'
GWFGLS <-
function (formula, data,
subset, weights, na.action,
Modified: pkg/MixABEL/man/FGLS.Rd
===================================================================
--- pkg/MixABEL/man/FGLS.Rd 2015-04-27 12:47:56 UTC (rev 1946)
+++ pkg/MixABEL/man/FGLS.Rd 2015-04-27 15:05:11 UTC (rev 1947)
@@ -1,3 +1,5 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fgls.R
\name{FGLS}
\alias{FGLS}
\title{Feasible GLS}
@@ -2,37 +4,31 @@
\usage{
- FGLS(Y, X, W = NULL, test = "wald",
- whichtest = c(FALSE, rep(TRUE, dim(X)[2] - 1)))
+FGLS(Y, X, W = NULL, test = "wald", whichtest = c(FALSE, rep(TRUE,
+ dim(X)[2] - 1)))
}
\arguments{
- \item{Y}{dependent variable}
+\item{Y}{dependent variable}
- \item{X}{design matrix (including intercept, if
- necessary)}
+\item{X}{design matrix (including intercept, if necessary)}
- \item{test}{test to be applied, one of 'wald', 'score' or
- 'robust'}
+\item{W}{for GLS, inverse variance-covariance matrix, as such returned by
+GenABEL's polygenic(...)$InvSigma, or NULL for LS}
- \item{whichtest}{which independent variables to be tested
- (set to 'TRUE')}
+\item{test}{test to be applied, one of 'wald', 'score' or 'robust'}
- \item{W}{for GLS, inverse variance-covariance matrix, as
- such returned by GenABEL's polygenic(...)$InvSigma, or
- NULL for LS}
+\item{whichtest}{which independent variables to be tested (set to 'TRUE')}
}
\value{
- List with elements 'beta' -- estimates fo the regression
- coefficients; 'V' -- variance covariance matrix for
- parameters estimates; 'T2' -- test statistics
- (distributed as Chi-squared under the null) for the
- testing of whichtest parameters; 'df' -- the number of
- degrees of freedom of the T2 test; 'tested' -- which
- parameters were tested with T2; 'meanColX' -- mean value
- of variable in columns of X; 'n' -- length of Y (==
- height of X)
+List with elements 'beta' -- estimates fo the regression
+coefficients; 'V' -- variance covariance matrix for parameters
+estimates; 'T2' -- test statistics (distributed as Chi-squared under
+the null) for the testing of whichtest parameters; 'df' -- the number of
+degrees of freedom of the T2 test; 'tested' -- which parameters were
+tested with T2; 'meanColX' -- mean value of variable in columns of X;
+'n' -- length of Y (== height of X)
}
\description{
- Feasible Generalised Least Squares
+Feasible Generalised Least Squares
}
\author{
- Yurii Aulchenko
+Yurii Aulchenko
}
Modified: pkg/MixABEL/man/FastMixedModel.Rd
===================================================================
--- pkg/MixABEL/man/FastMixedModel.Rd 2015-04-27 12:47:56 UTC (rev 1946)
+++ pkg/MixABEL/man/FastMixedModel.Rd 2015-04-27 15:05:11 UTC (rev 1947)
@@ -1,3 +1,5 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fastmixmod.R
\name{FastMixedModel}
\alias{FastMixedModel}
\title{fast mixed models}
@@ -2,30 +4,27 @@
\usage{
- FastMixedModel(Response, Explan, Kin, Covariates = NULL,
- nu_naught = 0, gamma_naught = 0)
+FastMixedModel(Response, Explan, Kin, Covariates = NULL, nu_naught = 0,
+ gamma_naught = 0)
}
\arguments{
- \item{Response}{is an n dimensional vector of Responses}
+\item{Response}{is an n dimensional vector of Responses}
- \item{Explan}{is an n*p matrix of Explanatory variables,
- each to be tested marginally (SNPS)}
+\item{Explan}{is an n*p matrix of Explanatory variables, each to be tested marginally (SNPS)}
- \item{Kin}{is the n*n kinship matrix}
+\item{Kin}{is the n*n kinship matrix}
- \item{Covariates}{is an n*k matrix of Covariates}
+\item{Covariates}{is an n*k matrix of Covariates}
- \item{nu_naught}{(and gamma_naught) are hyperparameters
- which control the heaviness of the tails of the test
- distribution (recommend leave them unchanged).}
+\item{nu_naught}{(and gamma_naught) are hyperparameters which control the heaviness
+of the tails of the test distribution (recommend leave them unchanged).}
- \item{gamma_naught}{(and nu_naught) are hyperparameters
- which control the heaviness of the tails of the test
- distribution (recommend leave them unchanged).}
+\item{gamma_naught}{(and nu_naught) are hyperparameters which control the heaviness
+of the tails of the test distribution (recommend leave them unchanged).}
}
\value{
- a list with values ...
+a list with values ...
}
\description{
- fast mixed models -- BETA VERSION If compiled against OMP
- this library can exploit multi-core parallelism Does not
- cope with missing data at present
+fast mixed models -- BETA VERSION
+If compiled against OMP this library can exploit multi-core parallelism
+Does not cope with missing data at present
}
@@ -89,12 +88,12 @@
plot(mms[,"chi2.1df"],fmm$chi.sq)
}
\author{
- William Astle \email{fio at where}
+William Astle \email{fio at where}
}
\references{
- reference to fill in
+reference to fill in
}
\seealso{
- mmscore
+mmscore
}
Modified: pkg/MixABEL/man/GWFGLS.Rd
===================================================================
--- pkg/MixABEL/man/GWFGLS.Rd 2015-04-27 12:47:56 UTC (rev 1946)
+++ pkg/MixABEL/man/GWFGLS.Rd 2015-04-27 15:05:11 UTC (rev 1947)
@@ -1,3 +1,5 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fgls.R
\name{GWFGLS}
\alias{GWFGLS}
\title{Genome-wide FGLS}
@@ -2,79 +4,68 @@
\usage{
- GWFGLS(formula, data, subset, weights, na.action,
- contrasts = NULL, offset, W = NULL, inverse = TRUE,
- na.SNP = "impute", mincall = 0.95, residuals = FALSE,
- test = "wald", model.SNP = "additive", genodata,
- gtcoding = "typed", verbosity = 1, varcov = FALSE,
- include.means = TRUE, singular = "ignore",
- with.lm = FALSE, old = FALSE)
+GWFGLS(formula, data, subset, weights, na.action, contrasts = NULL, offset,
+ W = NULL, inverse = TRUE, na.SNP = "impute", mincall = 0.95,
+ residuals = FALSE, test = "wald", model.SNP = "additive", genodata,
+ gtcoding = "typed", verbosity = 1, varcov = FALSE,
+ include.means = TRUE, singular = "ignore", with.lm = FALSE,
+ old = FALSE)
}
\arguments{
- \item{formula}{analysis formula; should contain special
- 'SNP' term}
+\item{formula}{analysis formula; should contain special 'SNP' term}
- \item{data}{phenotypic data frame, or 'gwaa.data-class'
- object}
+\item{data}{phenotypic data frame, or 'gwaa.data-class' object}
- \item{subset}{subset of data (individuals)}
+\item{subset}{subset of data (individuals)}
- \item{weights}{RESERVED FOR FURTURE USE}
+\item{weights}{RESERVED FOR FURTURE USE}
- \item{na.action}{RESERVED FOR FURTURE USE}
+\item{na.action}{RESERVED FOR FURTURE USE}
- \item{contrasts}{RESERVED FOR FURTURE USE}
+\item{contrasts}{RESERVED FOR FURTURE USE}
- \item{offset}{RESERVED FOR FURTURE USE}
+\item{offset}{RESERVED FOR FURTURE USE}
- \item{W}{for GLS, (inverse of) variance-covariance
- matrix, as such returned by GenABEL's
- polygenic(...)\$InvSigma, or NULL for LS}
+\item{W}{for GLS, (inverse of) variance-covariance matrix, as such returned by
+GenABEL's polygenic(...)\$InvSigma, or NULL for LS}
- \item{inverse}{wheather W is already inverted}
+\item{inverse}{wheather W is already inverted}
- \item{na.SNP}{how to deal with missing SNP data; 'impute'
- -- substitute with mean, 'drop' -- drop rows with missing
- genotypes}
+\item{na.SNP}{how to deal with missing SNP data; 'impute' -- substitute
+with mean, 'drop' -- drop rows with missing genotypes}
- \item{mincall}{minimall call rate for a SNP (if less, the
- SNP is dropped)}
+\item{mincall}{minimall call rate for a SNP (if less, the SNP is dropped)}
- \item{residuals}{use residuals for analysis? (faster, but
- less precise)}
+\item{residuals}{use residuals for analysis? (faster, but less precise)}
- \item{test}{test to be applied, one of 'wald', 'score' or
- 'robust'}
+\item{test}{test to be applied, one of 'wald', 'score' or 'robust'}
- \item{model.SNP}{SNP model to apply, one of
- c("additive","dominantB","recessiveB","overdominant","genotypic")}
+\item{model.SNP}{SNP model to apply, one of
+c("additive","dominantB","recessiveB","overdominant","genotypic")}
- \item{genodata}{genotypic data; can be missing if data is
- of 'gwaa.data-class'. Otherwise can be regular matrix or
- 'databel' matrix}
+\item{genodata}{genotypic data; can be missing if data is of 'gwaa.data-class'.
+Otherwise can be regular matrix or 'databel' matrix}
- \item{gtcoding}{one of c("typed","dose","probability")
- 'typed' -- coded with NA, 0, 1, 2}
+\item{gtcoding}{one of c("typed","dose","probability")
+'typed' -- coded with NA, 0, 1, 2}
- \item{verbosity}{what to report; 0 -- only test stats, 1
- -- test stats and estimates concerning 'whichtest'
- parameters, 2 -- test stats and estimates of all
- parameters}
+\item{verbosity}{what to report; 0 -- only test stats,
+1 -- test stats and estimates concerning 'whichtest' parameters,
+2 -- test stats and estimates of all parameters}
- \item{varcov}{wheather var-cov matrix for estimated
- parameters is to be reported}
+\item{varcov}{wheather var-cov matrix for estimated parameters
+is to be reported}
- \item{include.means}{weather mean values of predictors
- are to be reported}
+\item{include.means}{weather mean values of predictors are to
+be reported}
- \item{singular}{what to do with linear dependencies in X
- (now only 'ignore' implemented)}
+\item{singular}{what to do with linear dependencies in X (now only
+'ignore' implemented)}
- \item{with.lm}{whether LM should be run along (only test
- purposes; always falls back to 'old' R-only
- implementation)}
+\item{with.lm}{whether LM should be run along (only test purposes; always
+falls back to 'old' R-only implementation)}
- \item{old}{if TRUE, old R-only code implementation is
- running (testing purposes, slow)}
+\item{old}{if TRUE, old R-only code implementation is running (testing purposes,
+slow)}
}
\description{
- Genome-wide Feasible GLS
+Genome-wide Feasible GLS
}
@@ -123,10 +114,10 @@
aIN
aWN
complex_model <- GWFGLS(Y~age+sex*SNP,data=phdata(df),W=h2$InvSigma,
- genodata = gtReal,verbosity=2,varcov=TRUE,include.means=TRUE,model="genotypic")
+ genodata = gtReal,verbosity=2,varcov=TRUE,include.means=TRUE,model="genotypic")
complex_model
}
\author{
- Yurii Aulchenko
+Yurii Aulchenko
}
Modified: pkg/MixABEL/man/MixABEL-package.Rd
===================================================================
--- pkg/MixABEL/man/MixABEL-package.Rd 2015-04-27 12:47:56 UTC (rev 1946)
+++ pkg/MixABEL/man/MixABEL-package.Rd 2015-04-27 15:05:11 UTC (rev 1947)
@@ -1,16 +1,19 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/MixABEL-package.R
+\docType{package}
\name{MixABEL-package}
+\alias{"MixABEL"}
\alias{MixABEL-package}
\title{MixABEL package}
\usage{
- MixABEL-package()
+"MixABEL-package"()
}
\description{
- Package for fast (genome-wide) association analysis using
- mixed models. Main functions: \link{FastMixedModel},
- \link{GWFGLS}
+Package for fast (genome-wide) association analysis
+using mixed models. Main functions:
+\link{FastMixedModel}, \link{GWFGLS}
}
\author{
- Yurii Aulchenko, William Astle, Erik Roos, Marcel
- Kempenaar
+Yurii Aulchenko, William Astle, Erik Roos, Marcel Kempenaar
}
Modified: pkg/MixABEL/man/summaryFGLS.Rd
===================================================================
--- pkg/MixABEL/man/summaryFGLS.Rd 2015-04-27 12:47:56 UTC (rev 1946)
+++ pkg/MixABEL/man/summaryFGLS.Rd 2015-04-27 15:05:11 UTC (rev 1947)
@@ -1,3 +1,5 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/fgls.R
\name{summaryFGLS}
\alias{summaryFGLS}
\title{summary for FGLS}
@@ -2,27 +4,25 @@
\usage{
- summaryFGLS(x, verbosity = 1, varcov = FALSE,
- include.means = FALSE)
+summaryFGLS(x, verbosity = 1, varcov = FALSE, include.means = FALSE)
}
\arguments{
- \item{x}{object returned by FGLS function}
+\item{x}{object returned by FGLS function}
- \item{verbosity}{what to report; 0 -- only test stats, 1
- -- test stats and estimates concerning 'whichtest'
- parameters, 2 -- test stats and estimates of all
- parameters}
+\item{verbosity}{what to report; 0 -- only test stats,
+1 -- test stats and estimates concerning 'whichtest' parameters,
+2 -- test stats and estimates of all parameters}
- \item{varcov}{wheather var-cov matrix for estimated
- parameters is to be reported}
+\item{varcov}{wheather var-cov matrix for estimated parameters
+is to be reported}
- \item{include.means}{weather mean values of predictors
- are to be reported}
+\item{include.means}{weather mean values of predictors are to
+be reported}
}
\value{
- one-line summary of output from FGLS function
+one-line summary of output from FGLS function
}
\description{
- summary for Feasible GLS
+summary for Feasible GLS
}
\author{
- Yurii Aulchenko
+Yurii Aulchenko
}
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