[Genabel-commits] r817 - pkg/VariABEL/man

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

Author: maksim
Date: 2011-12-06 10:41:02 +0100 (Tue, 06 Dec 2011)
New Revision: 817

Modified:
   pkg/VariABEL/man/var_test_gwaa.Rd
Log:
change ecodding from ISO-8859 to ASCII. Otherwise checking fail...

Modified: pkg/VariABEL/man/var_test_gwaa.Rd
===================================================================
--- pkg/VariABEL/man/var_test_gwaa.Rd	2011-12-06 01:56:31 UTC (rev 816)
+++ pkg/VariABEL/man/var_test_gwaa.Rd	2011-12-06 09:41:02 UTC (rev 817)
@@ -2,63 +2,65 @@
 \alias{var_test_gwaa}
 \title{Function performs compariosn of genotypic variances.}
 \description{
-Presence of significant difference of genotypic variances points to possible 
-		Significant variance difference points to possible presence of interaction between a tested SNP and a factor (or set of factors).
+		Presence of significant difference of genotypic variances points to possible 
+						Significant variance difference points to possible presence of interaction between a tested SNP and a factor (or set of factors).
 }
 \usage{
-var_test_gwaa(formula, genodata, phenodata, genodata_info=NULL, testname="sqlm", analysis_type="AAvsABvsBB")
+		var_test_gwaa(formula, genodata, phenodata, genodata_info=NULL, testname="sqlm", analysis_type="AAvsABvsBB")
 }
 \arguments{\item{formula}{Regression model used for analysis. In the first stage linear regression is run to exclude main snp effect. In this stage adjustment for covariates is performed.}
-\item{genodata}{The genotypes data in format of genabel or databel object.}
-\item{phenodata}{The phenotypes data in format of data.frame object.}
-\item{genodata_info}{The file with snp information (name, position). Used if genodata is databel object.}
-\item{testname}{Name of variance heterogeneity test to perform. sqlm (for imputed genotype data), levene, and bartlett test are supported.}
-\item{analysis_type}{Type of analsysis to perform. AAvsABvsBB - additive model where B allele additivly increase risk, AAvsABandBB - group AA tested agains AB and BB, ABvsAAandBB - AB against AA and BB, BBvsAAandAB - BB against AA and AB. Only available for typed snps.}
+		\item{genodata}{The genotypes data in format of genabel or databel object.}
+		\item{phenodata}{The phenotypes data in format of data.frame object.}
+		\item{genodata_info}{The file with snp information (name, position). Used if genodata is databel object.}
+		\item{testname}{Name of variance heterogeneity test to perform. sqlm (for imputed genotype data), levene, and bartlett test are supported.}
+		\item{analysis_type}{Type of analsysis to perform. AAvsABvsBB - additive model where B allele additivly increase risk, AAvsABandBB - group AA tested agains AB and BB, ABvsAAandBB - AB against AA and BB, BBvsAAandAB - BB against AA and AB. Only available for typed snps.}
 }
 \details{
 
-The function var_test_gwaa tests for difference in genotypic variances. This difference points to presence of possible interaction between the tested SNP 
-and some factor. In the case sqlm test the analysis consists of two stage: firstly the regular GWA id done where regression analysis is performed with 
-covariates specified in the input parameter formula, in the second stage the regression analysis is performed with using residuals from the first stage and 
-a sno as a covariate.
+		The function var_test_gwaa tests for difference in genotypic variances. This difference points to presence of possible interaction between the tested SNP 
+				and some factor. In the case sqlm test the analysis consists of two stage: firstly the regular GWA id done where regression analysis is performed with 
+				covariates specified in the input parameter formula, in the second stage the regression analysis is performed with using residuals from the first stage and 
+				a sno as a covariate.
 }
 
 \value{
-	The ouput is a data.frame object. The table contains the chisq of variance heterogeneity test (the name is chisq) the effects and standart errors of all covariates included into regression model, 
-	main snp effect (the names are snp_eff and snp_se). In the case of sqlm test the columns snp_eff_dispertion and snp_se_dispertion contain
-	effect of a snp on squared vallues of a trait.
+			The ouput is a data.frame object. The table contains the chisq of variance heterogeneity test (the name is chisq) the effects and standart errors of all covariates included into regression model, 
+						main snp effect (the names are snp_eff and snp_se). In the case of sqlm test the columns snp_eff_dispertion and snp_se_dispertion contain
+									effect of a snp on squared vallues of a trait.
 
-	}
+										}
   
 
 %\references{ http://www.biomedcentral.com/1471-2156/11/92/abstract }
 \author{Maksim Struchalin}
 %\note{ ~~further notes~~ 
-%}
-%\seealso{
-%	\code{\link{var.meta}},
-%}
-\examples{
-	if (require(GenABEL)) {
-	data(srdta)
-	result1 <- var_test_gwaa(bt~qt1+qt2, genodata=gtdata(srdta), phenodata=phdata(srdta))
-	
+		%}
+		%\seealso{
+				%	\code{\link{var.meta}},
+						%}
+						\examples{
+									if (require(GenABEL)) {
+												data(srdta)
+															result1 <- var_test_gwaa(bt~qt1+qt2, genodata=gtdata(srdta), phenodata=phdata(srdta))
+																
 #if there is no covariates needed:
-	result2 <- var_test_gwaa("bt", genodata=gtdata(srdta), phenodata=phdata(srdta))
-	}
+																result2 <- var_test_gwaa("bt", genodata=gtdata(srdta), phenodata=phdata(srdta))
+																	}
 
-}
+						}
 
 \references{
 
-	Struchalin et al., Variance heterogeneity analysis for detection of potentially 
-	interacting genetic loci: method and its limitations. 
-	BMC Genetics 2010, 11:92, doi:10.1186/1471-2156-11-92
-	
-	Struchalin et al., An R package ÓVariABELÓ for genome-wide searching of
-	potentially interacting loci by testing genotypic variance heterogeneity. Submitted. 
-	
+			Struchalin et al., Variance heterogeneity analysis for detection of potentially 
+						interacting genetic loci: method and its limitations. 
+							BMC Genetics 2010, 11:92, doi:10.1186/1471-2156-11-92
+								
+								Struchalin et al., An R package VariABEL for genome-wide searching of
+									potentially interacting loci by testing genotypic variance heterogeneity. Submitted. 
+										
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
 \keyword{manip}
+
+