[Genabel-commits] r1090 - in pkg/GenABEL: . R

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

Author: yurii
Date: 2013-02-03 16:39:12 +0100 (Sun, 03 Feb 2013)
New Revision: 1090

Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/DESCRIPTION
   pkg/GenABEL/R/checkPackageVersionOnCRAN.R
   pkg/GenABEL/R/grammar.R
   pkg/GenABEL/R/zzz.R
Log:
bug in 'grammar', smaller default timeout in version checks

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2013-01-31 09:48:48 UTC (rev 1089)
+++ pkg/GenABEL/CHANGES.LOG	2013-02-03 15:39:12 UTC (rev 1090)
@@ -1,5 +1,9 @@
-***  v. 1.7-3 (2013.01.18)
+***  v. 1.7-4 (2013.02.03)
 
+(2013.02.03)
+Fixing bug in 'grammar': when using 'gamma', effects and s.e.s are not re-computed
+(bug reported by Xia Shen)
+
 (2013.01.18)
 Fixing bug in ztransform (if NA is present and formula used, NA's are kicked out)
 Changed the version number

Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION	2013-01-31 09:48:48 UTC (rev 1089)
+++ pkg/GenABEL/DESCRIPTION	2013-02-03 15:39:12 UTC (rev 1090)
@@ -2,7 +2,7 @@
 Type: Package
 Title: genome-wide SNP association analysis
 Version: 1.7-4
-Date: 2013-01-18
+Date: 2013-02-03
 Author: GenABEL project developers
 Contact: GenABEL project developers <genabel.project at gmail.com>
 Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru>

Modified: pkg/GenABEL/R/checkPackageVersionOnCRAN.R
===================================================================
--- pkg/GenABEL/R/checkPackageVersionOnCRAN.R	2013-01-31 09:48:48 UTC (rev 1089)
+++ pkg/GenABEL/R/checkPackageVersionOnCRAN.R	2013-02-03 15:39:12 UTC (rev 1090)
@@ -24,7 +24,7 @@
 #' @author Yurii Aulchenko
 #'
 checkPackageVersionOnCRAN <- function(packageName,baseUrlCRAN="http://cran.r-project.org/web/packages/", 
-		timeout = 5)
+		timeout = 2)
 {
 	# change default timout
 	svtmo <- options("timeout")

Modified: pkg/GenABEL/R/grammar.R
===================================================================
--- pkg/GenABEL/R/grammar.R	2013-01-31 09:48:48 UTC (rev 1089)
+++ pkg/GenABEL/R/grammar.R	2013-02-03 15:39:12 UTC (rev 1090)
@@ -88,10 +88,12 @@
 	if (method == "gamma") {
 		out <- qtscore(polyObject$pgresidualY,data=data,clambda=TRUE, ... )
 		# correct test and beta values
-		out at results[,"chi2.1df"] <- out[,"chi2.1df"]/polyObject$grammarGamma$Test
-		out at results[,"effB"] <- out[,"chi2.1df"]/polyObject$grammarGamma$Beta
+		out at results[,"chi2.1df"] <- out at results[,"chi2.1df"]/polyObject$grammarGamma$Test
+		out at results[,"effB"] <- out at results[,"effB"]/polyObject$grammarGamma$Beta
+		# re-compute standard errors (c2 = (b/se)^2; se = b/sqrt(c2))
+		out at results[,"se_effB"] <- abs(out at results[,"effB"])/sqrt(out at results[,"chi2.1df"])
 		# recompute p-values
-		out at results[,"P1df"] <- pchisq(out[,"chi2.1df"],df=1,lower.tail=FALSE)
+		out at results[,"P1df"] <- pchisq(out at results[,"chi2.1df"],df=1,lower.tail=FALSE)
 		# recompute Lambda
 		out at lambda <- estlambda(out[,"chi2.1df"],plot=FALSE,proportion=propPs)
 		if (out at lambda$estimate <= 1) {
@@ -109,6 +111,7 @@
 	# set uncorrectet stats to NA to avoid confusion
 	out at results[,"effAB"] <- out at results[,"effBB"] <- out at results[,"chi2.2df"] <- 
 			out at results[,"P2df"] <- NA
+	out at call <- match.call()
 	# return results
 	return(out);
 }
\ No newline at end of file

Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R	2013-01-31 09:48:48 UTC (rev 1089)
+++ pkg/GenABEL/R/zzz.R	2013-02-03 15:39:12 UTC (rev 1090)
@@ -5,7 +5,7 @@
 	#pkgVersion <- pkgDescription$Version
 	#pkgDate <- pkgDescription$Date
 	pkgVersion <- "1.7-4"
-	pkgDate <- "January 18, 2013"
+	pkgDate <- "February 03, 2013"
 	welcomeMessage <- paste(pkg," v. ",pkgVersion," (",pkgDate,") loaded\n",sep="")
 	# check if CRAN version is the same as loaded
 	cranVersion <- try( checkPackageVersionOnCRAN(pkg) )
@@ -24,7 +24,7 @@
 			"http://www.genabel.org/sites/default/files/version_and_news.html"
 	)
 	svtmo <- options("timeout")
-	options("timeout"=10)
+	options("timeout"=2)
 	tryRes1 <- 0; class(tryRes1) <- "try-error"
 	curaddr <- 1
 	while (class(tryRes1) == "try-error" && curaddr <= length(address) ) {