[Genabel-commits] r770 - in pkg/GenABEL: . R

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

Author: yurii
Date: 2011-08-25 00:31:21 +0200 (Thu, 25 Aug 2011)
New Revision: 770

Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/DESCRIPTION
   pkg/GenABEL/R/zzz.R
Log:
Update of 'polygenic_hglm' by Xia Shen. Quote:
We've updated the hglm package to version 1.2-2 recently on CRAN, where 
the major updates include:
- Sparse matrix implementation
- Multiple random effects
- Function hglm2() which accepts lme4-style formula input
In this update of polygenic_hglm() the speed could be slightly faster than 
before since the hglm() now uses sparse matrix technique (however I don't 
expect it to be much faster since the kinship matrix is always dense). Other 
modifications are:
- The current update of hglm package does not spit out profile log-likelihood 
since we haven't perfectly solved the likelihood computation for multiple random 
effects yet. But since polygenic_hglm() only needs one random effect (polygenic 
effect), I've re-implemented the likelihood computation directly in 
polygenic_hglm(), and no need to specify 'method = "REML"' anymore.
- In order to solve the problem from the forum about inputting formula as 
'y' or 'y ~ 1', I've added a check before creating the model.frame, so now 
 both types of inputs should work.

Added 'recodeChromosome' function, which must be handy when e.g. importing data 
from other software which uses integer for sex chromosomes and other non-autosomes
(X, Y, mt).

+> tutorial genetic data QC - list all options, do not use default?

'check.marker' added "none" (equal to ibs.mrk = -1); set "both" to default

Updated documentation for 'scan.glm.2D'.

Added GRAMMAR+ transformation and computation of GRAMMAR+ 
correction factors to 'polygenic'.

The default value for the stand option to convert.snp.tped() is now "u", 
instead of "+". Now convert.snp.tped() and convert.snp.ped() have the 
same defaults.

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2011-08-24 22:18:31 UTC (rev 769)
+++ pkg/GenABEL/CHANGES.LOG	2011-08-24 22:31:21 UTC (rev 770)
@@ -1,4 +1,4 @@
-*** v. 1.6-8 (2011.08.23)
+*** v. 1.6-8 (2011.08.25)
 
 Update of 'polygenic_hglm' by Xia Shen. Quote:
 We've updated the hglm package to version 1.2-2 recently on CRAN, where 

Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION	2011-08-24 22:18:31 UTC (rev 769)
+++ pkg/GenABEL/DESCRIPTION	2011-08-24 22:31:21 UTC (rev 770)
@@ -2,7 +2,7 @@
 Type: Package
 Title: genome-wide SNP association analysis
 Version: 1.6-8
-Date: 2011-07-15
+Date: 2011-08-25
 Author: GenABEL developers
 Maintainer: GenABEL developers <genabel-devel at r-forge.r-project.org>
 Depends: R (>= 2.10.0), methods, MASS

Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R	2011-08-24 22:18:31 UTC (rev 769)
+++ pkg/GenABEL/R/zzz.R	2011-08-24 22:31:21 UTC (rev 770)
@@ -1,6 +1,6 @@
 .onLoad <- function(lib, pkg) {
 	GenABEL.version <- "1.6-8"
-	cat("GenABEL v.",GenABEL.version,"(July 15, 2011) loaded\n")
+	cat("GenABEL v.",GenABEL.version,"(August 25, 2011) loaded\n")
 	
 	# check for updates and news
 	address <- c(