[Genabel-commits] r669 - in pkg/GenABEL: . R man

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

Author: yurii
Date: 2011-03-06 20:57:28 +0100 (Sun, 06 Mar 2011)
New Revision: 669

Modified:
   pkg/GenABEL/DESCRIPTION
   pkg/GenABEL/R/convert.snp.ped.R
   pkg/GenABEL/R/polygenic_hglm.R
   pkg/GenABEL/man/convert.snp.ped.Rd
   pkg/GenABEL/man/polygenic_hglm.Rd
Log:
resolving minor documentation issues, which popped up with R CMD check

Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION	2011-03-06 19:12:16 UTC (rev 668)
+++ pkg/GenABEL/DESCRIPTION	2011-03-06 19:57:28 UTC (rev 669)
@@ -6,7 +6,7 @@
 Author: Yurii Aulchenko et al.
 Maintainer: Yurii Aulchenko <i.aoultchenko at erasmusmc.nl>
 Depends: R (>= 2.10.0), methods, MASS
-Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm, MetABEL, ParallABEL, PredictABEL
+Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm, MetABEL, PredictABEL
 Description: a package for genome-wide association analysis between 
              quantitative or binary traits and single-nucleotide
              polymorphisms (SNPs). 

Modified: pkg/GenABEL/R/convert.snp.ped.R
===================================================================
--- pkg/GenABEL/R/convert.snp.ped.R	2011-03-06 19:12:16 UTC (rev 668)
+++ pkg/GenABEL/R/convert.snp.ped.R	2011-03-06 19:57:28 UTC (rev 669)
@@ -1,6 +1,6 @@
 "convert.snp.ped" <- 
 		function(pedfile,mapfile,outfile,format="premakeped",traits=1,
-				strand="u",bcast=10000000,wslash=FALSE,mapHasHeaderLine=FALSE) 
+				strand="u",bcast=10000000,wslash=FALSE,mapHasHeaderLine=TRUE) 
 {
 	
 	alcodes <- alleleID.codes()

Modified: pkg/GenABEL/R/polygenic_hglm.R
===================================================================
--- pkg/GenABEL/R/polygenic_hglm.R	2011-03-06 19:12:16 UTC (rev 668)
+++ pkg/GenABEL/R/polygenic_hglm.R	2011-03-06 19:57:28 UTC (rev 669)
@@ -14,7 +14,7 @@
 #' @param family a description of the error distribution and link function to be 
 #' used in the mean part of the model (see \code{\link{family}} for details of 
 #' family functions)
-#' @param ... other parameters passed to \code{\link{hglm}} call
+#' @param ... other parameters passed to 'hglm' call
 #' 
 #' @author Xia Shen, Yurii Aulchenko
 #' 

Modified: pkg/GenABEL/man/convert.snp.ped.Rd
===================================================================
--- pkg/GenABEL/man/convert.snp.ped.Rd	2011-03-06 19:12:16 UTC (rev 668)
+++ pkg/GenABEL/man/convert.snp.ped.Rd	2011-03-06 19:57:28 UTC (rev 669)
@@ -116,7 +116,7 @@
 }
 \examples{
 #
-# convert.snp.ped(ped="pedin.18",map="map.18",out="genos.raw")
+# convert.snp.ped(ped="pedin.18",mapfile="map.18",out="genos.raw")
 #
 }
 \keyword{IO}

Modified: pkg/GenABEL/man/polygenic_hglm.Rd
===================================================================
--- pkg/GenABEL/man/polygenic_hglm.Rd	2011-03-06 19:12:16 UTC (rev 668)
+++ pkg/GenABEL/man/polygenic_hglm.Rd	2011-03-06 19:57:28 UTC (rev 669)
@@ -22,7 +22,7 @@
 \item{family}{a description of the error distribution and link function to be 
 used in the mean part of the model (see \code{\link{family}} for details of 
 family functions)}
-\item{...}{other parameters passed to \code{\link{hglm}} call}}
+\item{...}{other parameters passed to 'hglm' call}}
 \examples{data(ge03d2ex.clean)
 df <- ge03d2ex.clean[,autosomal(ge03d2ex.clean)]
 gkin <- ibs(df,w="freq")