[Genabel-commits] r633 - in pkg/GenABEL: . R man

[noreply at r-forge.r-project.org]

Author: yurii
Date: 2011-01-27 18:11:15 +0100 (Thu, 27 Jan 2011)
New Revision: 633

Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/NAMESPACE
   pkg/GenABEL/R/merge.snp.data.R
   pkg/GenABEL/R/summary.scan.gwaa.R
   pkg/GenABEL/generate_documentation.R
   pkg/GenABEL/man/summary.gwaa.data.Rd
   pkg/GenABEL/man/summary.scan.gwaa.Rd
Log:
commented S4methods... in NAMESPACE to meet the 
request from the R-team; patched documentation for 
summary.scan.gwaa and summary.gwaa.data 
in order to avoid NOTE about S3methods "usage" 
section. This version will be submitted to CRAN if final checks will go smoothly.

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2011-01-27 16:45:17 UTC (rev 632)
+++ pkg/GenABEL/CHANGES.LOG	2011-01-27 17:11:15 UTC (rev 633)
@@ -1,5 +1,11 @@
 ***** v. 1.6-5 (2010.12.24)
 
+commented S4methods... in NAMESPACE to meet the 
+request from the R-team; patched documentation for 
+summary.scan.gwaa and summary.gwaa.data 
+in order to avoid NOTE about S3methods "usage" 
+section
+
 added extra checks for impute2databel to ensure that 
 sample file header is not used
 
@@ -8,7 +14,7 @@
 will be in output)
 
 Disabled check on intermediateXF in check.marker by setting intermediateXF=c(.5,.5) 
-by default. This should be better dealt with (see tracker '[#1210] intermediate 
+by default. This will be dealt with further (see tracker '[#1210] intermediate 
 inbreeding checks with check.marker' ) 
 
 patched Roxygen documentation for qtscore

Modified: pkg/GenABEL/NAMESPACE
===================================================================
--- pkg/GenABEL/NAMESPACE	2011-01-27 16:45:17 UTC (rev 632)
+++ pkg/GenABEL/NAMESPACE	2011-01-27 17:11:15 UTC (rev 633)
@@ -149,9 +149,9 @@
 S3method(plot,scan.gwaa)
 S3method(plot,scan.gwaa.2D)
 
-S4method('[',snp.data)
-S4method('[',gwaa.data)
-S4method('[',snp.mx)
+#S4method('[',snp.data)
+#S4method('[',gwaa.data)
+#S4method('[',snp.mx)
 
 S3method(as.character,gwaa.data)
 S3method(as.character,snp.data)

Modified: pkg/GenABEL/R/merge.snp.data.R
===================================================================
--- pkg/GenABEL/R/merge.snp.data.R	2011-01-27 16:45:17 UTC (rev 632)
+++ pkg/GenABEL/R/merge.snp.data.R	2011-01-27 17:11:15 UTC (rev 633)
@@ -17,7 +17,7 @@
 
 
 "merge.snp.data" <-
-function(x, y, ..., error_amount=1e+06, replacena=TRUE, forcestranduse=FALSE, sort = TRUE, intersected_snps_only=F) {
+function(x, y, ..., error_amount=1e+06, replacena=TRUE, forcestranduse=FALSE, sort = TRUE, intersected_snps_only=FALSE) {
 
 
 

Modified: pkg/GenABEL/R/summary.scan.gwaa.R
===================================================================
--- pkg/GenABEL/R/summary.scan.gwaa.R	2011-01-27 16:45:17 UTC (rev 632)
+++ pkg/GenABEL/R/summary.scan.gwaa.R	2011-01-27 17:11:15 UTC (rev 633)
@@ -1,19 +1,3 @@
-#' Shortcut to 'descriptives.scan'
-#' 
-#' Shortcut to 'descriptives.scan'
-#' 
-#' @param object object of class 'scan.gwaa' as generated by 
-#' \code{\link{qtscore}}, \code{\link{mlreg}}, etc.
-#' 
-#' @param ... arguments passed to \code{\link{descriptives.scan}}
-#' 
-#' @examples 
-#' data(srdta)
-#' x <- qtscore(qt2,srdta)
-#' summary(x)
-#' 
-#' @author Yurii Aulchenko
-#' 
 "summary.scan.gwaa" <- 
 		function(object,...) {
 	ret <- descriptives.scan(object, ... )

Modified: pkg/GenABEL/generate_documentation.R
===================================================================
--- pkg/GenABEL/generate_documentation.R	2011-01-27 16:45:17 UTC (rev 632)
+++ pkg/GenABEL/generate_documentation.R	2011-01-27 17:11:15 UTC (rev 633)
@@ -12,8 +12,9 @@
 		"mach2databel.R",
 		#"phdata.R",
 		"polygenic.R",
-		"qtscore.R",
-		"summary.scan.gwaa.R"
+		"qtscore.R"
+		#,
+		#"summary.scan.gwaa.R"
 )
 
 library(roxygen)

Modified: pkg/GenABEL/man/summary.gwaa.data.Rd
===================================================================
--- pkg/GenABEL/man/summary.gwaa.data.Rd	2011-01-27 16:45:17 UTC (rev 632)
+++ pkg/GenABEL/man/summary.gwaa.data.Rd	2011-01-27 17:11:15 UTC (rev 633)
@@ -5,7 +5,7 @@
 Summary of phenotypic and genotypic parts of GWAA data
 }
 \usage{
-summary.gwaa.data(object, ...)
+\method{summary}{gwaa.data}(object, ...) 
 }
 \arguments{
   \item{object}{object of class \code{\link{gwaa.data-class}}}

Modified: pkg/GenABEL/man/summary.scan.gwaa.Rd
===================================================================
--- pkg/GenABEL/man/summary.scan.gwaa.Rd	2011-01-27 16:45:17 UTC (rev 632)
+++ pkg/GenABEL/man/summary.scan.gwaa.Rd	2011-01-27 17:11:15 UTC (rev 633)
@@ -1,7 +1,9 @@
 \name{summary.scan.gwaa}
 \alias{summary.scan.gwaa}
 \title{Shortcut to 'descriptives...}
-\usage{summary.scan.gwaa(object, ...)}
+\usage{
+\method{summary}{scan.gwaa}(object, ...) 
+}
 \description{Shortcut to 'descriptives.scan'}
 \details{Shortcut to 'descriptives.scan'}
 \author{Yurii Aulchenko}