[Genabel-commits] r2072 - in pkg/MultiABEL: R man

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

Author: shenxia
Date: 2017-06-15 17:47:52 +0200 (Thu, 15 Jun 2017)
New Revision: 2072

Modified:
   pkg/MultiABEL/R/MultiLoad.R
   pkg/MultiABEL/R/Multivariate.R
   pkg/MultiABEL/man/MultiLoad.Rd
   pkg/MultiABEL/man/Multivariate.Rd
Log:
Uncomment some examples

Modified: pkg/MultiABEL/R/MultiLoad.R
===================================================================
--- pkg/MultiABEL/R/MultiLoad.R	2017-06-15 15:35:20 UTC (rev 2071)
+++ pkg/MultiABEL/R/MultiLoad.R	2017-06-15 15:47:52 UTC (rev 2072)
@@ -34,7 +34,7 @@
 #' \code{\link{Multivariate}}
 #' 
 #' @examples 
-#' \dontrun{
+#' 
 #' ## loading example gwaa.data in GenABEL
 #' require(GenABEL)
 #' data(ge03d2ex.clean)
@@ -43,6 +43,7 @@
 #' loaded <- MultiLoad(gwaa.data = ge03d2ex.clean, trait.cols = c(5, 6, 8), 
 #'                     covariate.cols = c(2, 3))
 #' 
+#' \dontrun{
 #' ## converting the same dataset into DatABEL format files
 #' require(DatABEL)
 #' write.table(phdata(ge03d2ex.clean), 'pheno.txt', col.names = TRUE, row.names = TRUE, 

Modified: pkg/MultiABEL/R/Multivariate.R
===================================================================
--- pkg/MultiABEL/R/Multivariate.R	2017-06-15 15:35:20 UTC (rev 2071)
+++ pkg/MultiABEL/R/Multivariate.R	2017-06-15 15:47:52 UTC (rev 2072)
@@ -30,17 +30,18 @@
 #' \code{\link{MultiLoad}}
 #' 
 #' @examples 
-#' \dontrun{
+#' 
 #' ## loading example gwaa.data in GenABEL
+#' require(GenABEL)
 #' data(ge03d2ex.clean)
 #' 
 #' ## running multivariate GWAS for 3 traits: height, weight, bmi
 #' loaded <- MultiLoad(gwaa.data = ge03d2ex.clean, trait.cols = c(5, 6, 8), 
 #'                     covariate.cols = c(2, 3))
 #' 
-#' ## running the multivariate GWAS again
+#' ## running the multivariate GWAS 
 #' res <- Multivariate(loaded)
-#' }
+#' 
 #' @aliases Multivariate, multivariate
 #' @keywords multivariate
 #' 
@@ -75,7 +76,7 @@
 	scan <- .Fortran('MultiSummaryLoopPrecise', k = as.integer(k), m = as.integer(m), nn = as.numeric(n), 
 			varg = x$cvg, betamat = betamat, R = x$cor.pheno, invR = solve(x$cor.pheno), D = matrix(0, m, m),
 			sdY = diag(sqrt(x$var.pheno)), invsdY = diag(1/sqrt(x$var.pheno)), sY = sqrt(x$var.pheno), 
-			b = betamat, s = betamat, pil = numeric(k), coef = betamat, PACKAGE = "MultiABEL")
+			b = betamat, s = betamat, pil = numeric(k), coef = betamat, ss = betamat, PACKAGE = "MultiABEL")
 	cat(' OK\n')
 	res$Beta.S <- scan$pil
 	scan$fstat <- res$Beta.S/m/(1 - res$Beta.S)*(n - m - 1)

Modified: pkg/MultiABEL/man/MultiLoad.Rd
===================================================================
--- pkg/MultiABEL/man/MultiLoad.Rd	2017-06-15 15:35:20 UTC (rev 2071)
+++ pkg/MultiABEL/man/MultiLoad.Rd	2017-06-15 15:47:52 UTC (rev 2072)
@@ -46,7 +46,7 @@
 DatABEL format input, individual IDs in \code{phenofile} and \code{genofile} have to match!
 }
 \examples{
-\dontrun{
+
 ## loading example gwaa.data in GenABEL
 require(GenABEL)
 data(ge03d2ex.clean)
@@ -55,6 +55,7 @@
 loaded <- MultiLoad(gwaa.data = ge03d2ex.clean, trait.cols = c(5, 6, 8), 
                     covariate.cols = c(2, 3))
 
+\dontrun{
 ## converting the same dataset into DatABEL format files
 require(DatABEL)
 write.table(phdata(ge03d2ex.clean), 'pheno.txt', col.names = TRUE, row.names = TRUE, 

Modified: pkg/MultiABEL/man/Multivariate.Rd
===================================================================
--- pkg/MultiABEL/man/Multivariate.Rd	2017-06-15 15:35:20 UTC (rev 2071)
+++ pkg/MultiABEL/man/Multivariate.Rd	2017-06-15 15:47:52 UTC (rev 2072)
@@ -34,18 +34,19 @@
 DatABEL format input, individual IDs in \code{phenofile} and \code{genofile} have to match!
 }
 \examples{
-\dontrun{
+
 ## loading example gwaa.data in GenABEL
+require(GenABEL)
 data(ge03d2ex.clean)
 
 ## running multivariate GWAS for 3 traits: height, weight, bmi
 loaded <- MultiLoad(gwaa.data = ge03d2ex.clean, trait.cols = c(5, 6, 8), 
                     covariate.cols = c(2, 3))
 
-## running the multivariate GWAS again
+## running the multivariate GWAS 
 res <- Multivariate(loaded)
+
 }
-}
 \references{
 Xia Shen, ..., Jim Wilson, Gordan Lauc, Yurii Aulchenko (2015).
 Multi-omic-variate analysis identified novel loci associated with