[Genabel-commits] r1271 - in pkg/GenABEL: . R man

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

Author: yurii
Date: 2013-07-19 14:05:18 +0200 (Fri, 19 Jul 2013)
New Revision: 1271

Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/R/impute2databel.R
   pkg/GenABEL/R/mach2databel.R
   pkg/GenABEL/R/minimac2databel.R
   pkg/GenABEL/man/add.plot.Rd
Log:
data type warnings in *2databel's

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2013-07-14 21:34:31 UTC (rev 1270)
+++ pkg/GenABEL/CHANGES.LOG	2013-07-19 12:05:18 UTC (rev 1271)
@@ -1,5 +1,9 @@
 ***  v. 1.7-7
 
+(2013.07.19)
+Added warning that *2databel's may not produce output in desired data type 
+and fall onto float 
+
 (2013.06.29)
 Changed the 'polygenic' nullification threshold to 1e-8
 

Modified: pkg/GenABEL/R/impute2databel.R
===================================================================
--- pkg/GenABEL/R/impute2databel.R	2013-07-14 21:34:31 UTC (rev 1270)
+++ pkg/GenABEL/R/impute2databel.R	2013-07-19 12:05:18 UTC (rev 1271)
@@ -32,6 +32,10 @@
   if (missing(outfile))
     outfile <- genofile
 
+  if (dataOutType != "FLOAT") 
+      warning("The non-float dataOutType os not fully supported; your outputs may be in 'FLOAT'...",
+              immediate. = TRUE);
+
   ## extract snp names (varnames)
   ## if (tmpname != "")
   ##     text2databel(infile=genofile,outfile=outfile,

Modified: pkg/GenABEL/R/mach2databel.R
===================================================================
--- pkg/GenABEL/R/mach2databel.R	2013-07-14 21:34:31 UTC (rev 1270)
+++ pkg/GenABEL/R/mach2databel.R	2013-07-19 12:05:18 UTC (rev 1271)
@@ -31,6 +31,9 @@
 	if (missing(imputedgenofile))
 		stop("mldose file must be specified")
 	if (missing(outfile)) outfile <- imputedgenofile
+    if (dataOutType != "FLOAT") 
+        warning("The non-float dataOutType os not fully supported; your outputs may be in 'FLOAT'...",
+                immediate. = TRUE);
 # extract snp names (varnames)
 	tmpname <- ""
 	if (!missing(mlinfofile))

Modified: pkg/GenABEL/R/minimac2databel.R
===================================================================
--- pkg/GenABEL/R/minimac2databel.R	2013-07-14 21:34:31 UTC (rev 1270)
+++ pkg/GenABEL/R/minimac2databel.R	2013-07-19 12:05:18 UTC (rev 1271)
@@ -34,7 +34,10 @@
   if (missing(imputedgenofile))
     stop("A dose file must be specified")
   if (missing(outfile)) outfile <- imputedgenofile
-  ## extract snp names (varnames)
+  if (dataOutType != "FLOAT") 
+      warning("The non-float dataOutType os not fully supported; your outputs may be in 'FLOAT'...",
+              immediate. = TRUE);
+## extract snp names (varnames)
   tmpname <- ""
   if (!missing(infofile))
     {

Modified: pkg/GenABEL/man/add.plot.Rd
===================================================================
--- pkg/GenABEL/man/add.plot.Rd	2013-07-14 21:34:31 UTC (rev 1270)
+++ pkg/GenABEL/man/add.plot.Rd	2013-07-19 12:05:18 UTC (rev 1271)
@@ -44,4 +44,4 @@
 a1 <- qtscore(bt,srdta,snps=c(1:100))
 add.plot(a1,col="red",type="l")
 }
-\keyword{hplot}% at least one, from doc/KEYWORDS
+\keyword{aplot}% at least one, from doc/KEYWORDS