[Genabel-commits] r628 - in pkg/GenABEL: . R man

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

Author: yurii
Date: 2010-12-24 16:20:14 +0100 (Fri, 24 Dec 2010)
New Revision: 628

Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/R/check.marker.R
   pkg/GenABEL/man/check.marker.Rd
Log:
set intermediateXF=c(.5,.5) as default in check.marker as a way to temporarily compensate for negative effect of bug '[#1210] intermediate inbreeding checks with check.marker'

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2010-12-17 11:18:46 UTC (rev 627)
+++ pkg/GenABEL/CHANGES.LOG	2010-12-24 15:20:14 UTC (rev 628)
@@ -1,5 +1,9 @@
-***** v. 1.6-5 (2010.12.07)
+***** v. 1.6-5 (2010.12.24)
 
+Disabled check on intermediateXF in check.marker by setting intermediateXF=c(.5,.5) 
+by default. This should be better dealt with (see tracker '[#1210] intermediate 
+inbreeding checks with check.marker' ) 
+
 patched Roxygen documentation for qtscore
 
 use of 'setTxtProgressBar' in qtscore with times > 1 to indicate progress

Modified: pkg/GenABEL/R/check.marker.R
===================================================================
--- pkg/GenABEL/R/check.marker.R	2010-12-17 11:18:46 UTC (rev 627)
+++ pkg/GenABEL/R/check.marker.R	2010-12-24 15:20:14 UTC (rev 628)
@@ -5,7 +5,7 @@
 			maf, p.level=-1, 
 			fdrate = 0.2, odds = 1000, hweidsubset, redundant="no", minconcordance = 2.0, 
 			qoption="bh95",imphetasmissing=TRUE,XXY.call=0.8, 
-			intermediateXF = c(0.2,0.8)) {
+			intermediateXF = c(0.5,0.5)) {
 
 	if (is(data,"gwaa.data")) data <- data at gtdata
 	if (!is(data,"snp.data")) stop("data argument should be of type gwaa.data or snp.data");

Modified: pkg/GenABEL/man/check.marker.Rd
===================================================================
--- pkg/GenABEL/man/check.marker.Rd	2010-12-17 11:18:46 UTC (rev 627)
+++ pkg/GenABEL/man/check.marker.Rd	2010-12-24 15:20:14 UTC (rev 628)
@@ -14,7 +14,7 @@
 		ibs.threshold = 0.95, ibs.mrk = 2000, ibs.exclude="lower", maf, p.level = -1, fdrate = 0.2, 
 		odds = 1000, hweidsubset, redundant = "no", 
 		minconcordance = 2.0, qoption = "bh95", imphetasmissing = TRUE, XXY.call=0.8,
-		intermediateXF = c(0.2, 0.8)) 
+		intermediateXF = c(0.5, 0.5)) 
 }
 \arguments{
   \item{data}{gwaa.data or snp.data object}
@@ -50,7 +50,8 @@
 			be treated as missing genotypes in the QC procedure}
   \item{XXY.call}{What proportion of Y-chromosome markers should be called to consider that 
 			Y-chromosome is present (in presence of XX)}
-  \item{intermediateXF}{X-chromosomal F to be considered 'intermediate' and regarded as error}
+  \item{intermediateXF}{X-chromosomal F to be considered 'intermediate' and regarded as error; 
+  			currently use of default disables this check}
 }
 \details{
 	In this procedure, sex errors are identified initally and then