[Genabel-commits] r1240 - pkg/GenABEL/inst/unitTests

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

Author: lckarssen
Date: 2013-06-03 14:22:51 +0200 (Mon, 03 Jun 2013)
New Revision: 1240

Modified:
   pkg/GenABEL/inst/unitTests/runit.exports.R
Log:
Code layout changes (added some spaces after comma's and split a few long lines) in GenABEL's runit.exports.R unit tests. 

No functional changes. 


Modified: pkg/GenABEL/inst/unitTests/runit.exports.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.exports.R	2013-06-03 12:13:29 UTC (rev 1239)
+++ pkg/GenABEL/inst/unitTests/runit.exports.R	2013-06-03 12:22:51 UTC (rev 1240)
@@ -4,9 +4,9 @@
 #
 
 if(FALSE) {
-	## Not really needed, but can be handy when writing tests
-	library(RUnit)
-	library(GenABEL)
+  ## Not really needed, but can be handy when writing tests
+  library(RUnit)
+  library(GenABEL)
 }
 
 ### do not run
@@ -22,77 +22,84 @@
 
 test.exports <- function()
 {
-	data(ge03d2.clean)
-	nTestIds <- sample(c(10:min(100,nids(ge03d2.clean))),1)
-	nTestSnps <- sample(c(10:min(1000,nsnps(ge03d2.clean))),1)
-	dta <- ge03d2.clean[sort(sample(1:nids(ge03d2.clean),nTestIds)),
-			sort(sample(1:nsnps(ge03d2.clean),nTestSnps))]
-	
-	export.plink(dta,filebasename="tmpOld",dpieceFun="old")
-	export.plink(dta,filebasename="tmpNew",dpieceFun="new")
-	xO <- read.table(file="tmpOld.ped",head=FALSE,strings=FALSE)
-	xN <- read.table(file="tmpNew.ped",head=FALSE,strings=FALSE)
-	checkIdentical(xN,xO)
-	xO <- read.table(file="tmpOld.map",head=FALSE,strings=FALSE)
-	xN <- read.table(file="tmpNew.map",head=FALSE,strings=FALSE)
-	checkIdentical(xN,xO)
-	xO <- read.table(file="tmpOld.map.ext",head=FALSE,strings=FALSE)
-	xN <- read.table(file="tmpNew.map.ext",head=FALSE,strings=FALSE)
-	checkIdentical(xN,xO)
-	
-	unlink("tmpOld*")
-	unlink("tmpNew*")
-	
-	export.merlin(dta,pedfile="tmpOld.ped",datafile="tmpOld.dat",
-			mapfile="tmpOld.map",dpieceFun="old")
-	export.merlin(dta,pedfile="tmpNew.ped",datafile="tmpNew.dat",
-			mapfile="tmpNew.map",dpieceFun="new")
-	xO <- read.table(file="tmpOld.ped",head=FALSE,strings=FALSE)
-	xN <- read.table(file="tmpNew.ped",head=FALSE,strings=FALSE)
-	checkIdentical(xN,xO)
-	xO <- read.table(file="tmpOld.map",head=FALSE,strings=FALSE)
-	xN <- read.table(file="tmpNew.map",head=FALSE,strings=FALSE)
-	checkIdentical(xN,xO)
-	xO <- read.table(file="tmpOld.map.ext",head=FALSE,strings=FALSE)
-	xN <- read.table(file="tmpNew.map.ext",head=FALSE,strings=FALSE)
-	checkIdentical(xN,xO)
-	xO <- read.table(file="tmpOld.dat",head=FALSE,strings=FALSE)
-	xN <- read.table(file="tmpNew.dat",head=FALSE,strings=FALSE)
-	checkIdentical(xN,xO)
-	
-	unlink("tmpOld*")
-	unlink("tmpNew*")	
-	
-	export.plink(dta,filebasename="tmpTrans",transpose=TRUE)
-	convert.snp.tped(tpedfile="tmpTrans.tped",tfamfile="tmpTrans.tfam",out="tmpTrans.raw")
-	xBack <- load.gwaa.data(gen="tmpTrans.raw",phe="tmpTrans.phe",id="IID")
-	strand(xBack) <- strand(dta)
-	phdata(xBack) <- phdata(xBack)[,-1]
-	sameCode <- which(coding(dta) == coding(xBack))
-	checkIdentical(xBack[,sameCode],dta[,sameCode])
-	swappedCode <- which(refallele(dta)==effallele(xBack) & effallele(dta)==refallele(xBack))
-	for (i in swappedCode) {
-		gtDta <- c(2,1,0)[as.vector(as.numeric(dta[,i]))+1]
-		gtBack <- as.vector(as.numeric(xBack[,i]))
-		print(checkIdentical(gtBack,gtDta))
-	}
-	
-	unlink("tmpTrans*")
-	
+  data(ge03d2.clean)
+  nTestIds <- sample(c(10:min(100, nids(ge03d2.clean))), 1)
+  nTestSnps <- sample(c(10:min(1000, nsnps(ge03d2.clean))), 1)
+  dta <- ge03d2.clean[sort(sample(1:nids(ge03d2.clean), nTestIds)),
+                      sort(sample(1:nsnps(ge03d2.clean), nTestSnps))]
+
+  export.plink(dta, filebasename="tmpOld", dpieceFun="old")
+  export.plink(dta, filebasename="tmpNew", dpieceFun="new")
+  xO <- read.table(file="tmpOld.ped", head=FALSE, strings=FALSE)
+  xN <- read.table(file="tmpNew.ped", head=FALSE, strings=FALSE)
+  checkIdentical(xN, xO)
+  xO <- read.table(file="tmpOld.map", head=FALSE, strings=FALSE)
+  xN <- read.table(file="tmpNew.map", head=FALSE, strings=FALSE)
+  checkIdentical(xN, xO)
+  xO <- read.table(file="tmpOld.map.ext", head=FALSE, strings=FALSE)
+  xN <- read.table(file="tmpNew.map.ext", head=FALSE, strings=FALSE)
+  checkIdentical(xN, xO)
+
+  unlink("tmpOld*")
+  unlink("tmpNew*")
+
+  export.merlin(dta, pedfile="tmpOld.ped", datafile="tmpOld.dat",
+                mapfile="tmpOld.map", dpieceFun="old")
+  export.merlin(dta, pedfile="tmpNew.ped", datafile="tmpNew.dat",
+                mapfile="tmpNew.map", dpieceFun="new")
+  xO <- read.table(file="tmpOld.ped", head=FALSE, strings=FALSE)
+  xN <- read.table(file="tmpNew.ped", head=FALSE, strings=FALSE)
+  checkIdentical(xN, xO)
+
+  xO <- read.table(file="tmpOld.map", head=FALSE, strings=FALSE)
+  xN <- read.table(file="tmpNew.map", head=FALSE, strings=FALSE)
+  checkIdentical(xN, xO)
+
+  xO <- read.table(file="tmpOld.map.ext", head=FALSE, strings=FALSE)
+  xN <- read.table(file="tmpNew.map.ext", head=FALSE, strings=FALSE)
+  checkIdentical(xN, xO)
+
+  xO <- read.table(file="tmpOld.dat", head=FALSE, strings=FALSE)
+  xN <- read.table(file="tmpNew.dat", head=FALSE, strings=FALSE)
+  checkIdentical(xN, xO)
+
+  unlink("tmpOld*")
+  unlink("tmpNew*")
+
+  export.plink(dta, filebasename="tmpTrans", transpose=TRUE)
+  convert.snp.tped(tpedfile="tmpTrans.tped",
+                   tfamfile="tmpTrans.tfam",
+                   out="tmpTrans.raw")
+  xBack <- load.gwaa.data(gen="tmpTrans.raw", phe="tmpTrans.phe", id="IID")
+  strand(xBack) <- strand(dta)
+  phdata(xBack) <- phdata(xBack)[, -1]
+  sameCode <- which(coding(dta) == coding(xBack))
+  checkIdentical(xBack[, sameCode], dta[, sameCode])
+
+  swappedCode <- which(refallele(dta)==effallele(xBack) &
+                       effallele(dta)==refallele(xBack))
+  for (i in swappedCode) {
+    gtDta <- c(2, 1, 0)[as.vector(as.numeric(dta[, i]))+1]
+    gtBack <- as.vector(as.numeric(xBack[, i]))
+    print(checkIdentical(gtBack, gtDta))
+  }
+
+  unlink("tmpTrans*")
 }
 
+
 test.export.merlin.bug2525 <- function()
 {
-	data(srdta)
-	export.merlin(
-			srdta[,1:2],dpieceFun="new",
-			mapfile="tmpNew.map",pedfile="tmpNew.ped",datafile="tmpNew.dat"
-	)
-	export.merlin(
-			srdta[,1:2],dpieceFun="old",
-			mapfile="tmpOld.map",pedfile="tmpOld.ped",datafile="tmpOld.dat"
-	)
-	xO <- read.table(file="tmpOld.ped",head=FALSE,strings=FALSE)
-	xN <- read.table(file="tmpNew.ped",head=FALSE,strings=FALSE)
-	checkIdentical(xN,xO)
+  data(srdta)
+  export.merlin(
+    srdta[, 1:2], dpieceFun="new",
+    mapfile="tmpNew.map", pedfile="tmpNew.ped", datafile="tmpNew.dat"
+    )
+  export.merlin(
+    srdta[, 1:2], dpieceFun="old",
+    mapfile="tmpOld.map", pedfile="tmpOld.ped", datafile="tmpOld.dat"
+    )
+  xO <- read.table(file="tmpOld.ped", head=FALSE, strings=FALSE)
+  xN <- read.table(file="tmpNew.ped", head=FALSE, strings=FALSE)
+  checkIdentical(xN, xO)
 }