[Genabel-commits] r813 - in pkg/GenABEL: . R inst/unitTests

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

Author: yurii
Date: 2011-12-05 17:23:11 +0100 (Mon, 05 Dec 2011)
New Revision: 813

Added:
   pkg/GenABEL/inst/unitTests/runit.sortmap.internal.R
Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/R/sortmap.internal.R
   pkg/GenABEL/inst/unitTests/runit.merge.R
Log:
Addressed bug [#1673], added unit test runit.sortmap.internal.R/test.sortmap.internal.bug1673


Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2011-12-05 15:33:44 UTC (rev 812)
+++ pkg/GenABEL/CHANGES.LOG	2011-12-05 16:23:11 UTC (rev 813)
@@ -1,7 +1,13 @@
 *** v. 1.7-0 (2011.11.15)
 
-Addressed bug [#1676], added unit test runit.merge.R/test.merge.bug1676
+Addressed bug [#1673] (bug in load.gwaa.data and export.merlin when 
+sorting is enabled, filed in by Daniel Taliun), added unit test 
+runit.sortmap.internal.R/test.sortmap.internal.bug1673
 
+Addressed bug [#1676] (regression in merge of gwaa.data, phenotypes 
+don't get merged correctly; filed in by Lennart Karssen), added unit 
+test runit.merge.R/test.merge.bug1676
+
 Added 'KS' method to estimate lambda in 'estlambda'. Generates rather 
 good results (under null) and may be considered as default option in the future, 
 after testing under the alternative. 
@@ -16,10 +22,11 @@
 
 export.merlin, export.plink now runs much faster (exports on C++ code)
 
-Bug [#1641] reported by Karl Froner fixed. Now GenABEL 
-deals with exceptional situation in merge.snp.data / monomorphic part; 
-added case of no overlap in SNPs (skip monomorphic staff then). RUnit 
-regression test runit.merge.R/test.merge.bug1641 added.   
+Bug [#1641] (regression bug with merge.snp.data in version 1.6.9; 
+filed in by Karl Froner) fixed. Now GenABEL deals with exceptional 
+situation in merge.snp.data / monomorphic part; added case of no overlap 
+in SNPs (skip monomorphic staff then). RUnit regression test 
+runit.merge.R/test.merge.bug1641 added.   
 
 Modifications in 'estlambda': plot=FALSE by default, added option 
 to estimate Lambda with median method; added option 'filter' for 

Modified: pkg/GenABEL/R/sortmap.internal.R
===================================================================
--- pkg/GenABEL/R/sortmap.internal.R	2011-12-05 15:33:44 UTC (rev 812)
+++ pkg/GenABEL/R/sortmap.internal.R	2011-12-05 16:23:11 UTC (rev 813)
@@ -1,16 +1,16 @@
 "sortmap.internal" <-
-function(chrom,map,delta=1) {
+		function(chrom,map,delta=1) {
 	chnum <- chrom.char2num(chrom)
-
+	
 	ix <- order(chnum,map)
-
+	
 	map <- map[ix]
-
-   off <- c(0,map[1:(length(map)-1)])
+	
+	off <- c(0,map[1:(length(map)-1)])
 	off <- map - off
 	off[which(off<=0)] <- delta
 	cummap <- cumsum(off)
-
+	
 	out <- list()
 	out$ix <- ix
 	out$cummap <- cummap
@@ -20,11 +20,15 @@
 
 chrom.char2num <- function(chrom) {
 	chrom <- as.character(chrom)
-   chdesU <- unique(chrom)
-   chnumU <- suppressWarnings(as.numeric(chdesU))
-   chCHU <- sort(chdesU[is.na(chnumU)])
-	maxch <- max(chnumU,na.rm=T)
-   j <- 1
+	chdesU <- unique(chrom)
+	chnumU <- suppressWarnings(as.numeric(chdesU))
+	chCHU <- sort(chdesU[is.na(chnumU)])
+	if (any(!is.na(chnumU))) {
+		maxch <- max(chnumU,na.rm=T)
+	} else {
+		maxch <- 0
+	}
+	j <- 1
 	for (i in chCHU) {
 		chrom[which(chrom==i)] <- as.character(maxch+j)
 		j <- j + 1

Modified: pkg/GenABEL/inst/unitTests/runit.merge.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.merge.R	2011-12-05 15:33:44 UTC (rev 812)
+++ pkg/GenABEL/inst/unitTests/runit.merge.R	2011-12-05 16:23:11 UTC (rev 813)
@@ -39,4 +39,4 @@
 	phdata(xy)
 	checkIdentical(phdata(xy)[1:dim(phdata(x1))[1],],phdata(x1))
 	checkIdentical(phdata(xy)[(dim(phdata(x1))[1]+1):(dim(phdata(x1))[1]+dim(phdata(x2))[1]),],phdata(x2))
-}
\ No newline at end of file
+}

Added: pkg/GenABEL/inst/unitTests/runit.sortmap.internal.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.sortmap.internal.R	                        (rev 0)
+++ pkg/GenABEL/inst/unitTests/runit.sortmap.internal.R	2011-12-05 16:23:11 UTC (rev 813)
@@ -0,0 +1,39 @@
+### --- Test setup ---
+#
+# regression test
+#
+
+if(FALSE) {
+	## Not really needed, but can be handy when writing tests
+	library(RUnit)
+	library(GenABEL)
+}
+
+### do not run
+#stop("SKIP THIS TEST")
+###
+
+### ---- common functions and data -----
+
+#source(paste("../inst/unitTests/shared_functions.R"))
+#source(paste(path,"/shared_functions.R",sep=""))
+
+### --- Test functions ---
+
+test.sortmap.internal.bug1673 <- function()
+{
+	source("../R/sortmap.internal.R")
+	nmrkInChr <- c(7,5,3)
+	chrLevels <- c("cH1","X","Y")
+	chroms <- mappos <- rep(NA,sum(nmrkInChr))
+	k <- 1
+	for (i in 1:length(nmrkInChr)) {
+		for (j in seq(nmrkInChr[i],1,-1)) {
+			chroms[k] <- chrLevels[i]
+			mappos[k] <- j
+			k <- k + 1
+		}
+	}
+	a <- sortmap.internal(chroms,mappos)
+	checkTrue( all(is.finite(a$chnum)) )
+}


Property changes on: pkg/GenABEL/inst/unitTests/runit.sortmap.internal.R
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Added: svn:mime-type
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