[Genabel-commits] r820 - in pkg/VariABEL: R man src/VARlib

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

Author: maksim
Date: 2011-12-06 11:14:08 +0100 (Tue, 06 Dec 2011)
New Revision: 820

Modified:
   pkg/VariABEL/R/var_test_gwaa.R
   pkg/VariABEL/man/var_test_gwaa.Rd
   pkg/VariABEL/src/VARlib/supplementary_functions.h
   pkg/VariABEL/src/VARlib/var_homogeneity_test_C.cpp
Log:
change sqlm into svlm as it is used in the paper

Modified: pkg/VariABEL/R/var_test_gwaa.R
===================================================================
--- pkg/VariABEL/R/var_test_gwaa.R	2011-12-06 10:08:26 UTC (rev 819)
+++ pkg/VariABEL/R/var_test_gwaa.R	2011-12-06 10:14:08 UTC (rev 820)
@@ -24,7 +24,7 @@
 #_____________________________________________________________________________________________________________________________
 #Available for user function for genome-wide testing variance homogeneity of trait's distribution.
 #
-"var_test_gwaa" <- function(formula, genodata, phenodata, genodata_info=NULL, testname="sqlm", analysis_type="AAvsABvsBB")
+"var_test_gwaa" <- function(formula, genodata, phenodata, genodata_info=NULL, testname="svlm", analysis_type="AAvsABvsBB")
 {
 
 
@@ -32,8 +32,8 @@
 else if(testname == "levene") {testname <- 1}
 else if(testname == "likelihood") {testname <- 2}
 else if(testname == "kolmogorov_smirnov") {testname <- 3}
-else if(testname == "sqlm") {testname <- 4}
-else {stop(paste(testname, "is unsupportive type of test. Only levene, and sqlm are supported."))}
+else if(testname == "svlm") {testname <- 4}
+else {stop(paste(testname, "is unsupportive type of test. Only levene, and svlm are supported."))}
 
 
 if(analysis_type == "AAvsABvsBB") {analysis_type <- 0}

Modified: pkg/VariABEL/man/var_test_gwaa.Rd
===================================================================
--- pkg/VariABEL/man/var_test_gwaa.Rd	2011-12-06 10:08:26 UTC (rev 819)
+++ pkg/VariABEL/man/var_test_gwaa.Rd	2011-12-06 10:14:08 UTC (rev 820)
@@ -6,26 +6,26 @@
 						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="svlm", 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{testname}{Name of variance heterogeneity test to perform. svlm (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 
+				and some factor. In the case svlm 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
+						main snp effect (the names are snp_eff and snp_se). In the case of svlm test the columns snp_eff_dispertion and snp_se_dispertion contain
 									effect of a snp on squared vallues of a trait.
 
 										}

Modified: pkg/VariABEL/src/VARlib/supplementary_functions.h
===================================================================
--- pkg/VariABEL/src/VARlib/supplementary_functions.h	2011-12-06 10:08:26 UTC (rev 819)
+++ pkg/VariABEL/src/VARlib/supplementary_functions.h	2011-12-06 10:14:08 UTC (rev 820)
@@ -170,7 +170,7 @@
 const short unsigned int levene = 1;
 const short unsigned int likelihood = 2;
 const short unsigned int kolmogorov_smirnov = 3;
-const short unsigned int sqlm=4;
+const short unsigned int svlm=4;
 
 
 

Modified: pkg/VariABEL/src/VARlib/var_homogeneity_test_C.cpp
===================================================================
--- pkg/VariABEL/src/VARlib/var_homogeneity_test_C.cpp	2011-12-06 10:08:26 UTC (rev 819)
+++ pkg/VariABEL/src/VARlib/var_homogeneity_test_C.cpp	2011-12-06 10:14:08 UTC (rev 820)
@@ -74,7 +74,7 @@
 
 
 
-if(*testname != sqlm)
+if(*testname != svlm)
 	{
 	break_trait_up_into_groups(&trait_groups, snp, trait, nids_, *analys_type_, is_trait_na);