[Genabel-commits] r2030 - pkg/RepeatABEL/vignettes

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

Author: larsronn
Date: 2015-11-28 11:47:53 +0100 (Sat, 28 Nov 2015)
New Revision: 2030

Removed:
   pkg/RepeatABEL/vignettes/.Rhistory
Log:
.Rhistory removed

Deleted: pkg/RepeatABEL/vignettes/.Rhistory
===================================================================
--- pkg/RepeatABEL/vignettes/.Rhistory	2015-11-24 07:25:13 UTC (rev 2029)
+++ pkg/RepeatABEL/vignettes/.Rhistory	2015-11-28 10:47:53 UTC (rev 2030)
@@ -1,44 +0,0 @@
-library(RepeatABEL)
-data(Phen.Data) #Phenotype data with repeated observations
-data(gen.data) #GenABEL object including IDs and marker genotypes
-GWAS1 <- rGLS(y ~ age + sex, genabel.data = gen.data, phenotype.data = Phen.Data)
-summary(GWAS1 at call$hglm)
-str(GWAS1 at call$hglm)
-GWAS1 at call$hglm$SummVC2
-GWAS1 at call$hglm$SummVC1
-GWAS1 at call$hglm$SummVC2[[1]]
-GWAS1 at call$hglm$varRanef
-GWAS1 at call$hglm$varFix
-cat("The genotypic and permanent env. variance components are", VCGWAS1b at call$hglm$varRanef,", resp.","\n")
-cat("The residual variance is", VCGWAS1b at call$hglm$varFix,".","\n")
-fixed=y ~ age + sex
-Mod1 <- preFitModel(fixed, random=~1|id,
-genabel.data = gen.data,
-phenotype.data = Phen.Data,
-corStruc=list( id=list("GRM","Ind") ))
-GWAS1b <- rGLS(fixed, genabel.data = gen.data,
-phenotype.data = Phen.Data, V = Mod1$V)
-cat("The genotypic and permanent env. variance components are", VCGWAS1b at call$hglm$varRanef,", resp.","\n")
-cat("The residual variance is", VCGWAS1b at call$hglm$varFix,".","\n")
-cat("The genotypic and permanent env. variance components are", GWAS1b at call$hglm$varRanef,", resp.","\n")
-cat("The residual variance is", GWAS1b at call$hglm$varFix,".","\n")
-GWAS1b at call$hglm$varRanef
-GWAS1 at call$hglm$varRanef
-Mod1 at call$hglm$varRanef
-str(Mod1)
-cat("The estimate and SE for the genotypic variance:", GWAS1 at call$hglm$SummVC2[[1]],", resp.","\n")
-cat("Confidence interval: [", GWAS1 at call$hglm$SummVC2[[1]][1] - 1.96*GWAS1 at call$hglm$SummVC2[[1]][2],",",GWAS1 at call$hglm$SummVC2[[1]][1] + 1.96*GWAS1 at call$hglm$SummVC2[[1]][2],"\n")
-cat("The estimate and SE for the genotypic variance on a natural log scale:", GWAS1 at call$hglm$SummVC2[[1]],", resp.","\n")
-cat("Confidence interval: [", exp( GWAS1 at call$hglm$SummVC2[[1]][1] - 1.96*GWAS1 at call$hglm$SummVC2[[1]][2] ) ,",",exp( GWAS1 at call$hglm$SummVC2[[1]][1] + 1.96*GWAS1 at call$hglm$SummVC2[[1]][2] ),"]",\n")
-cat("The estimate and SE for the genotypic variance on a natural log scale:", logVCE[1],"and",logVCE[2],"\n")
-cat("Confidence interval: [", exp( logVCE[1] - 1.96*logVCE[2] ) ,",",exp( logVCE[1] + 1.96*logVCE[2] ),"]","\n")
-logVCE <- GWAS1 at call$hglm$SummVC2[[1]]
-cat("The estimate and SE for the genotypic variance on a natural log scale:", logVCE[1],"and",logVCE[2],"\n")
-cat("Confidence interval: [", exp( logVCE[1] - 1.96*logVCE[2] ) ,",",exp( logVCE[1] + 1.96*logVCE[2] ),"]","\n")
-cat("The estimate and SE for the genotypic variance on a natural log scale:", logVCE[1],"and",logVCE[2],", resp.", "\n")
-cat("Confidence interval: [", exp( logVCE[1] - 1.96*logVCE[2] ) ,",",exp( logVCE[1] + 1.96*logVCE[2] ),"]","\n")
-logVCE <- GWAS1 at call$hglm$SummVC2[[1]]
-cat("The estimate and SE for the genotypic variance on a natural log scale:", logVCE[1],"and",logVCE[2],", resp.", "\n")
-cat("Confidence interval: [", exp( logVCE[1] - 1.96*logVCE[2] ) , "," , exp( logVCE[1] + 1.96*logVCE[2] ) , "]" , "\n")
-cat("The genotypic and permanent env. variance components are", GWAS1 at call$hglm$varRanef,", resp.","\n")
-cat("The residual variance is", GWAS1 at call$hglm$varFix,".","\n")