[Genabel-commits] r668 - in pkg/GenABEL: . R man

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

Author: yurii
Date: 2011-03-06 20:12:16 +0100 (Sun, 06 Mar 2011)
New Revision: 668

Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/DESCRIPTION
   pkg/GenABEL/R/polygenic_hglm.R
   pkg/GenABEL/man/convert.snp.illumina.Rd
   pkg/GenABEL/man/convert.snp.mach.Rd
Log:
clean-up documentation + some cosmetics

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2011-03-06 19:11:17 UTC (rev 667)
+++ pkg/GenABEL/CHANGES.LOG	2011-03-06 19:12:16 UTC (rev 668)
@@ -1,5 +1,11 @@
-*** v. 1.6-6 (2011.02.25)
+*** v. 1.6-6 (2011.03.06)
 
+Changes convert.snp.mach documentation to reflect the fact that 
+the map-file should have header; changes to convert.snp.illumina 
+documentation to reflect the nature of the data better; added 
+option 'mapHasHeaderLine' to convert.snp.ped and updated documentation
+(resolving feature request #1317).  
+
 With suggestion and guidance from Xia Shen, added procedure 'polygenic_hglm'.
 At the moment very experimental, and needs to pass checks before can be released. 
 

Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION	2011-03-06 19:11:17 UTC (rev 667)
+++ pkg/GenABEL/DESCRIPTION	2011-03-06 19:12:16 UTC (rev 668)
@@ -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
+Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm, MetABEL, ParallABEL, PredictABEL
 Description: a package for genome-wide association analysis between 
              quantitative or binary traits and single-nucleotide
              polymorphisms (SNPs). 

Modified: pkg/GenABEL/R/polygenic_hglm.R
===================================================================
--- pkg/GenABEL/R/polygenic_hglm.R	2011-03-06 19:11:17 UTC (rev 667)
+++ pkg/GenABEL/R/polygenic_hglm.R	2011-03-06 19:12:16 UTC (rev 668)
@@ -93,4 +93,4 @@
 	
 	class(out) <- "polygenic"
 	out
-}
\ No newline at end of file
+}

Modified: pkg/GenABEL/man/convert.snp.illumina.Rd
===================================================================
--- pkg/GenABEL/man/convert.snp.illumina.Rd	2011-03-06 19:11:17 UTC (rev 667)
+++ pkg/GenABEL/man/convert.snp.illumina.Rd	2011-03-06 19:12:16 UTC (rev 668)
@@ -9,7 +9,7 @@
 }
 \arguments{
   \item{infile}{
-	Pre-makeped linkage genotypic data file name
+	Map + genotypic data file name
 	}
   \item{outfile}{
 	Output data file

Modified: pkg/GenABEL/man/convert.snp.mach.Rd
===================================================================
--- pkg/GenABEL/man/convert.snp.mach.Rd	2011-03-06 19:11:17 UTC (rev 667)
+++ pkg/GenABEL/man/convert.snp.mach.Rd	2011-03-06 19:12:16 UTC (rev 668)
@@ -2,7 +2,8 @@
 \alias{convert.snp.mach}
 \title{function to convert genotypic data from MACH format to internal data format}
 \description{
-Converts genotypic data from MACH format to internal genotypic data formated file
+Converts genotypic data from MACH format to internal genotypic data formated file 
+(NOT recommended)
 }
 \usage{
 convert.snp.mach(pedfile, mapfile, infofile, outfile, quality = 0.9, column.quality = 7, strand = "+", ...)
@@ -12,7 +13,7 @@
 	File with genotypic data from MACH (geno or mlgeno)
 	}
   \item{mapfile}{
-	Name of the map file
+	Name of the map file (note that header line should be included)
 	}
   \item{infofile}{
 	Name MACH info-file
@@ -41,6 +42,11 @@
 	This is a simple script converting the MACH data with  \code{\link{convert.snp.ped}},
 	re-loading data, and filtering the snp.data object based on quality as specified in 
 	MACH info-file
+	
+	Note that it is NOT recommended to process imputations results with this procedure, 
+	as uncertainty inherent to imputations is lost after processing ("hard" calls are made)!
+	For the purposes of GWA analysis, we recommend procedures, which make direct use of 
+	estimated allele dose or genotypic probabilities.
 }
 \value{
 	Does not return any value, but writes file with GenABEL raw data