[Genabel-commits] r946 - in pkg/GenABEL: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 29 23:17:16 CEST 2012
Author: yurii
Date: 2012-08-29 23:17:16 +0200 (Wed, 29 Aug 2012)
New Revision: 946
Modified:
pkg/GenABEL/CHANGES.LOG
pkg/GenABEL/DESCRIPTION
pkg/GenABEL/R/grammar.R
pkg/GenABEL/R/zzz.R
pkg/GenABEL/man/export.impute.Rd
pkg/GenABEL/man/grammar.Rd
Log:
preparing CRAN release of GenA package 1.7-1
Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG 2012-08-28 07:28:43 UTC (rev 945)
+++ pkg/GenABEL/CHANGES.LOG 2012-08-29 21:17:16 UTC (rev 946)
@@ -1,3 +1,9 @@
+(2012.08.29, YA)
+
+Small changes related to CRAN release of 1.7-1; this release is to be
+updated to 1.7-2 as soon as the Grammar-Gamma paper is published and
+some feedback is collected for the 1.7-1
+
(2012.08.15, YA)
Small updates to documentation, verifying that checks are passed.
Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION 2012-08-28 07:28:43 UTC (rev 945)
+++ pkg/GenABEL/DESCRIPTION 2012-08-29 21:17:16 UTC (rev 946)
@@ -2,7 +2,7 @@
Type: Package
Title: genome-wide SNP association analysis
Version: 1.7-1
-Date: 2012-01-11
+Date: 2012-08-29
Author: GenABEL developers
Maintainer: GenABEL project <genabel.project at gmail.com>
Depends: R (>= 2.10.0), methods, MASS, utils
Modified: pkg/GenABEL/R/grammar.R
===================================================================
--- pkg/GenABEL/R/grammar.R 2012-08-28 07:28:43 UTC (rev 945)
+++ pkg/GenABEL/R/grammar.R 2012-08-29 21:17:16 UTC (rev 946)
@@ -14,7 +14,7 @@
#' the model; also, the estimates of regression coefficients are biased (the
#' same as in 'raw' GRAMMAR).
#'
-#' GRAMMAR-Gamma ('gamma' argument) solves these problems, producing
+#' GRAMMAR-Gamma (default 'gamma' argument) solves these problems, producing
#' correct distribution of the test statistic, interpretable value of GC Lambda,
#' and unbiased estimates of the regression coefficients. All together, the
#' default 'gamma' method is recommended for use.
@@ -24,7 +24,7 @@
#' @param method to be used, one of 'gamma','gc', or 'raw'
#' @param propPs proportion of non-corrected P-values used to estimate the inflation factor Lambda,
#' passed directly to the \code{\link{estlambda}}
-#' @param ... arguments passed to the function used for computations
+#' @param ... arguments passed to the function used for computations,
#' (\code{\link{qtscore}})
#'
#' @return Object of scan.gwaa-class
@@ -42,11 +42,12 @@
#' A genomic background based method for association analysis in related individuals.
#' PLoS One. 2007 Dec 5;2(12):e1274.
#'
-#' GRAMMAR-Gamma: Svisheva et al., submitted
+#' GRAMMAR-Gamma: Svisheva GR, Axenovich TI, Belonogova MN, van Duijn CM, Aulchenko YS.
+#' Rapid variance componentsÐbased method for whole-genome association analysis.
+#' (in press)
#'
#' @examples
-#' # ge03d2 is rather bad data set for demonstration,
-#' # because this is a population-based study
+#' # Using clean ge03d2 data
#' data(ge03d2.clean)
#' #take half for speed
#' ge03d2.clean <- ge03d2.clean[1:300,]
Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R 2012-08-28 07:28:43 UTC (rev 945)
+++ pkg/GenABEL/R/zzz.R 2012-08-29 21:17:16 UTC (rev 946)
@@ -5,7 +5,7 @@
#pkgVersion <- pkgDescription$Version
#pkgDate <- pkgDescription$Date
pkgVersion <- "1.7-1"
- pkgDate <- "January 11, 2012"
+ pkgDate <- "August 29, 2012"
welcomeMessage <- paste(pkg," v. ",pkgVersion," (",pkgDate,") loaded\n",sep="")
# check if CRAN version is the same as loaded
cranVersion <- checkPackageVersionOnCRAN(pkg)
Modified: pkg/GenABEL/man/export.impute.Rd
===================================================================
--- pkg/GenABEL/man/export.impute.Rd 2012-08-28 07:28:43 UTC (rev 945)
+++ pkg/GenABEL/man/export.impute.Rd 2012-08-29 21:17:16 UTC (rev 946)
@@ -44,7 +44,7 @@
}
\examples{
\dontrun{
-load(srdta)
+data(srdta)
export.impute(srdta[1:50,1:3])
}
}
Modified: pkg/GenABEL/man/grammar.Rd
===================================================================
--- pkg/GenABEL/man/grammar.Rd 2012-08-28 07:28:43 UTC (rev 945)
+++ pkg/GenABEL/man/grammar.Rd 2012-08-29 21:17:16 UTC (rev 946)
@@ -18,7 +18,7 @@
to the \code{\link{estlambda}}}
\item{...}{arguments passed to the function used for
- computations (\code{\link{qtscore}})}
+ computations, (\code{\link{qtscore}})}
}
\value{
Object of scan.gwaa-class
@@ -42,15 +42,14 @@
goodness of the model; also, the estimates of regression
coefficients are biased (the same as in 'raw' GRAMMAR).
- GRAMMAR-Gamma ('gamma' argument) solves these problems,
- producing correct distribution of the test statistic,
- interpretable value of GC Lambda, and unbiased estimates
- of the regression coefficients. All together, the default
- 'gamma' method is recommended for use.
+ GRAMMAR-Gamma (default 'gamma' argument) solves these
+ problems, producing correct distribution of the test
+ statistic, interpretable value of GC Lambda, and unbiased
+ estimates of the regression coefficients. All together,
+ the default 'gamma' method is recommended for use.
}
\examples{
-# ge03d2 is rather bad data set for demonstration,
-# because this is a population-based study
+# Using clean ge03d2 data
data(ge03d2.clean)
#take half for speed
ge03d2.clean <- ge03d2.clean[1:300,]
@@ -91,7 +90,8 @@
background based method for association analysis in
related individuals. PLoS One. 2007 Dec 5;2(12):e1274.
- GRAMMAR-Gamma: Svisheva et al., submitted
+ GRAMMAR-Gamma: Svisheva GR, Axenovich TI, Belonogova MN,
+ van Duijn CM, Aulchenko YS. (in press)
}
\seealso{
\code{\link{polygenic}}, \code{\link{mmscore}},
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