[Genabel-commits] r837 - in pkg/GenABEL: . R inst/unitTests man src/GAlib
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 11 19:39:37 CET 2012
Author: yurii
Date: 2012-01-11 19:39:37 +0100 (Wed, 11 Jan 2012)
New Revision: 837
Modified:
pkg/GenABEL/CHANGES.LOG
pkg/GenABEL/DESCRIPTION
pkg/GenABEL/R/ibs.R
pkg/GenABEL/R/zzz.R
pkg/GenABEL/generate_documentation.R
pkg/GenABEL/inst/unitTests/report.html
pkg/GenABEL/inst/unitTests/report.txt
pkg/GenABEL/inst/unitTests/reportSummary.txt
pkg/GenABEL/man/ibs.Rd
pkg/GenABEL/src/GAlib/gwaa.c
Log:
new dev-version 1.7-1, including new "eVar" option for ibs function
Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/CHANGES.LOG 2012-01-11 18:39:37 UTC (rev 837)
@@ -1,3 +1,9 @@
+*** v. 1.7-1 (2012.01.11)
+
+Added option weight = "eVar" to 'ibs'. This uses empirical variance of
+genotypes when estimating kinship matrix. This is useful when working with
+such data as Arabidopsis.
+
*** v. 1.7-0 (2011.12.20)
Addressed bug [#1383] (message about upgrade on loading the library
Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/DESCRIPTION 2012-01-11 18:39:37 UTC (rev 837)
@@ -1,8 +1,8 @@
Package: GenABEL
Type: Package
Title: genome-wide SNP association analysis
-Version: 1.7-0
-Date: 2011-12-20
+Version: 1.7-1
+Date: 2012-01-11
Author: GenABEL developers
Maintainer: GenABEL developers <genabel.project at gmail.com>
Depends: R (>= 2.10.0), methods, MASS, utils
Modified: pkg/GenABEL/R/ibs.R
===================================================================
--- pkg/GenABEL/R/ibs.R 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/R/ibs.R 2012-01-11 18:39:37 UTC (rev 837)
@@ -1,3 +1,98 @@
+#' Computes (average) Idenity-by-State for a set of people and markers
+#'
+#' Given a set of SNPs, computes a matrix of average IBS for a group
+#' of individuals.
+#' This function facilitates quality control of genomic data.
+#' E.g. people with exteremly high (close to 1) IBS may indicate
+#' duplicated samples (or twins), simply high values of IBS may
+#' indicate relatives.
+#'
+#' When weight "freq" is used, IBS for a pair of people i and j is computed as
+#'
+#' \deqn{
+#' f_{i,j} = \Sigma_k \frac{(x_{i,k} - p_k) * (x_{j,k} - p_k)}{(p_k * (1 - p_k))}
+#' }
+#'
+#' where k changes from 1 to N = number of SNPs GW, \eqn{x_{i,k}} is
+#' a genotype of ith person at the kth SNP, coded as 0, 1/2, 1 and
+#' \eqn{p_k} is the frequency
+#' of the "+" allele. This apparently provides an unbiased estimate of the
+#' kinship coefficient.
+#'
+#' With "eVar" option above formula changes by using ( 2 * empirical variance
+#' of the genotype ) in the denominator
+#'
+#' Only with "freq" option monomorphic SNPs are regarded as non-informative.
+#'
+#' ibs() operation may be very lengthy for a large number of people.
+#'
+#' @return A (Npeople X Npeople) matrix giving average IBS (kinship) values
+#' between a pair below the diagonal and number of SNP genotype
+#' measured for both members of the pair above the diagonal.
+#'
+#' On the diagonal, homozygosity 0.5*(1+inbreeding) is provided.
+#'
+#' attr(computedobject,"Var") returns variance (replacing the
+#' diagonal when the object is used by \code{\link{egscore}}
+#'
+#' @param data object of \code{\link{snp.data-class}}
+#' @param snpsubset Index, character or logical vector with subset of SNPs to run analysis on.
+#' If missing, all SNPs from \code{data} are used for analysis.
+#' @param idsubset IDs of people to be analysed.
+#' If missing, all people from \code{data} are used for analysis.
+#' @param cross.idsubset Parameter allowing parallel implementation. Not to be used normally.
+#' If supplied together with idsubset, the ibs/kinship for all pairs between
+#' idsubset and cross.idsubset computed.
+#' @param weight "no" for direct IBS computations, "freq" to weight by allelic frequency
+#' asuming HWE and "eVar" for empirical variance to be used
+#' @param snpfreq when option weight="freq" used, you can provide
+#' fixed allele frequencies
+#'
+#' @author Yurii Aulchenko
+#'
+#' @seealso \code{\link{check.marker}}, \code{\link{summary.snp.data}},
+#' \code{\link{snp.data-class}}
+#'
+#' @examples
+#' data(ge03d2c)
+#'
+#' # compute IBS based on a random sample of 1000 autosomal marker
+#' selectedSnps <- sample(autosomal(ge03d2c),1000,replace=FALSE)
+#' a <- ibs(ge03d2c,snps=selectedSnps)
+#' a[1:5,1:5]
+#' mds <- cmdscale(as.dist(1-a))
+#' plot(mds)
+#' # identify smaller cluster of outliers
+#' km <- kmeans(mds,centers=2,nstart=1000)
+#' cl1 <- names(which(km$cluster==1))
+#' cl2 <- names(which(km$cluster==2))
+#' if (length(cl1) > length(cl2)) cl1 <- cl2;
+#' cl1
+#' # PAINT THE OUTLIERS IN RED
+#' points(mds[cl1,],pch=19,col="red")
+#' # compute genomic kinship matrix to be used with e.g. polygenic, mmscore, etc
+#' a <- ibs(ge03d2c,snps=sample(autosomal(ge03d2c),1000,replace=FALSE),weight="freq")
+#' a[1:5,1:5]
+#' # now replace diagonal with EIGENSTRAT-type of diaganal to be used for egscore
+#' diag(a) <- hom(ge03d2c[,autosomal(ge03d2c)])$Var
+#' a[1:5,1:5]
+#' ##############################
+#' # compare 'freq' with 'eVar'
+#' ##############################
+#' ibsFreq <- ibs(ge03d2c[,autosomal(ge03d2c)], weight="freq")
+#' ibsEvar <- ibs(ge03d2c[,autosomal(ge03d2c)], weight="eVar")
+#' mdsEvar <- cmdscale( as.dist( 0.5 - ibsEvar ) )
+#' plot(mdsEvar)
+#' outliers <- (mdsEvar[,1]>0.1)
+#' ibsFreq[upper.tri(ibsFreq,diag=TRUE)] <- NA
+#' ibsEvar[upper.tri(ibsEvar,diag=TRUE)] <- NA
+#' plot(ibsEvar,ibsFreq)
+#' points(ibsEvar[outliers,outliers],ibsFreq[outliers,outliers],col="red")
+#'
+#' @keywords htest
+#'
+#' '
+
"ibs" <-
function (data,snpsubset,idsubset=NULL,cross.idsubset=NULL,weight="no",snpfreq=NULL) {
# idsubset, cross.idsubset: should be real names, not indexes!
@@ -13,7 +108,7 @@
snpfreq <- summary(data)[,"Q.2"]
}
- wargs <- c("no","freq","homo")
+ wargs <- c("no","freq","homo","eVar")
if (!(match(weight,wargs,nomatch=0)>0)) {
out <- paste("weight argument should be one of",wargs,"\n")
stop(out)
@@ -31,6 +126,9 @@
rm(smr);gc();
homodiag <- rep(1.0,nids(data))
option = 2
+ } else if (weight == "eVar") {
+ homodiag <- rep(0.5,nids(data))
+ option = 3
} else {
stop("'weight' argument value not recognised")
}
@@ -74,8 +172,8 @@
as.integer(length(idset2.num)), as.integer(idset2.num-1), as.double(snpfreq),
as.integer(option), sout = double(2*length(idset1.num)*length(idset2.num)),
PACKAGE="GenABEL")$sout
- } else if (option==2) {
- stop("option 2 only availabel in optimized version")
+ } else if (option>1) {
+ stop("parallel execution facilities with options >1 only available in optimized version")
} else {
stop("unknown 'weight' option")
}
Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/R/zzz.R 2012-01-11 18:39:37 UTC (rev 837)
@@ -4,8 +4,8 @@
#pkgDescription <- packageDescription(pkg)
#pkgVersion <- pkgDescription$Version
#pkgDate <- pkgDescription$Date
- pkgVersion <- "1.7-0"
- pkgDate <- "December 20, 2011"
+ pkgVersion <- "1.7-1"
+ pkgDate <- "January 11, 2012"
welcomeMessage <- paste(pkg," v. ",pkgVersion," (",pkgDate,") loaded\n",sep="")
# check if CRAN version is the same as loaded
cranVersion <- checkPackageVersionOnCRAN(pkg)
Modified: pkg/GenABEL/generate_documentation.R
===================================================================
--- pkg/GenABEL/generate_documentation.R 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/generate_documentation.R 2012-01-11 18:39:37 UTC (rev 837)
@@ -13,6 +13,7 @@
"GenABEL-package.R",
"generateOffspring.R",
"getLogLikelihoodGivenRelation.R",
+ "ibs.R",
"impute2databel.R",
"impute2mach.R",
#"LiLogCC.R",
Modified: pkg/GenABEL/inst/unitTests/report.html
===================================================================
--- pkg/GenABEL/inst/unitTests/report.html 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/inst/unitTests/report.html 2012-01-11 18:39:37 UTC (rev 837)
@@ -1,11 +1,11 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/transitional.dtd">
-<html><head><title>RUNIT TEST PROTOCOL--Tue Dec 6 13:20:55 2011</title>
+<html><head><title>RUNIT TEST PROTOCOL--Wed Jan 11 19:21:05 2012</title>
</head>
-<body><h1 TRUE>RUNIT TEST PROTOCOL--Tue Dec 6 13:20:55 2011</h1>
+<body><h1 TRUE>RUNIT TEST PROTOCOL--Wed Jan 11 19:21:05 2012</h1>
<p>Number of test functions: 18</p>
<p>Number of errors: 0</p>
-<p style=color:red>Number of failures: 2</p>
+<p>Number of failures: 0</p>
<hr>
<h3 TRUE>1 Test suite</h3>
<table border="1" width="60%" >
@@ -17,47 +17,28 @@
<tr><td><a href="#GenABEL unit testing">GenABEL unit testing</a></td>
<td>18</td>
<td>0</td>
-<td bgcolor="red">2</td>
+<td>0</td>
</tr>
</table>
<hr>
-<h3 TRUE>Failures</h3>
-<table border="1" width="100%" >
-<tr><th width="30%">Test suite : test function</th>
-<th width="70%">message</th>
-</tr>
-<tr><td><a href="#GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.exports.R_test.exports">GenABEL unit testing : test.exports</a></td>
-<td>Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
-</td>
-</tr>
-<tr><td><a href="#GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polylik.R_test.polylik">GenABEL unit testing : test.polylik</a></td>
-<td>Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
- Mean relative difference: 1.756053e-08
-</td>
-</tr>
-</table>
-<hr>
<h3 TRUE>Details</h3>
<p><a name="GenABEL unit testing"><h5 TRUE>Test Suite: GenABEL unit testing</h5>
-</a>Test function regexp: ^test.+<br/>Test file regexp: ^runit.+\.[rR]$<br/>Involved directory:<br/>/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests<br/><ul><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R">Test file: runit.convert.snp.ped.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.ped.R_test.convert.snp.ped">test.convert.snp.ped: (0 checks) ... OK (0.12 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R">Test file: runit.convert.snp.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.R_test.convert.snp">test.convert.snp: (4 checks) ... OK (1.49 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R">Test file: runit.descriptives.trait.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.descriptives.trait.R_test.descriptives.trait">test.descriptives.trait: (1 checks) ... OK (0.43 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R">Test file: runit.exports.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.exports.R_test.exports"><u style=color:red>test.exports: FAILURE !! (check number 8) </u></a>Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
-<br/></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R">Test file: runit.findRelatives.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.findRelatives.R_test.findRelatives">test.findRelatives: (10 checks) ... OK (45.05 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R">Test file: runit.impute2xxx_large.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx_large.R_test.impute2xxx_large">test.impute2xxx_large: (0 checks) ... OK (0.03 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R">Test file: runit.impute2xxx.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx.R_test.impute2databel">test.impute2databel: (23 checks) ... OK (1.15 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.iterator.R">Test file: runit.iterator.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.iterator.R_test.qtscore">test.qtscore: (0 checks) ... OK (0 seconds)<br/></a></li><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.iterator.R_test.summary_snp_data">test.summary_snp_data: (3 checks) ... OK (8.34 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mach2databel.R">Test file: runit.mach2databel.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.mach2databel.R_test.mach2databel">test.mach2databel: (8 checks) ... OK (0.97 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.merge.R">Test file: runit.merge.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.merge.R_test.merge.bug1641">test.merge.bug1641: (0 checks) ... OK (0.17 seconds)<br/></a></li><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.merge.R_test.merge.bug1676">test.merge.bug1676: (2 checks) ... OK (0.2 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mmscore.R">Test file: runit.mmscore.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.mmscore.R_test.exports">test.exports: (1 checks) ... OK (0.65 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polygenic.R">Test file: runit.polygenic.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polygenic.R_test.polygenic.Bug1322">test.polygenic.Bug1322: (2 checks) ... OK (1.05 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polylik.R">Test file: runit.polylik.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polylik.R_test.polylik"><u style=color:red>test.polylik: FAILURE !! (check number 4) </u></a>Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
- Mean relative difference: 1.756053e-08
-<br/></li></ul></li></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.recodeChromosome.R">Test file: runit.recodeChromosome.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.recodeChromosome.R_test.recodeChromosome">test.recodeChromosome: (8 checks) ... OK (0.19 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.sortmap.internal.R">Test file: runit.sortmap.internal.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.sortmap.internal.R_test.sortmap.internal.bug1673">test.sortmap.internal.bug1673: (1 checks) ... OK (0 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.strandModify.R">Test file: runit.strandModify.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.strandModify.R_test.strandModify">test.strandModify: (2 checks) ... OK (0.05 seconds)<br/></a></li></ul></li></ul><hr>
+</a>Test function regexp: ^test.+<br/>Test file regexp: ^runit.+\.[rR]$<br/>Involved directory:<br/>/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests<br/><ul><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R">Test file: runit.convert.snp.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.R_test.convert.snp">test.convert.snp: (4 checks) ... OK (1.43 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R">Test file: runit.convert.snp.ped.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.ped.R_test.convert.snp.ped">test.convert.snp.ped: (0 checks) ... OK (0.02 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R">Test file: runit.descriptives.trait.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.descriptives.trait.R_test.descriptives.trait">test.descriptives.trait: (1 checks) ... OK (0.47 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R">Test file: runit.exports.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.exports.R_test.exports">test.exports: (50 checks) ... OK (1.21 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R">Test file: runit.findRelatives.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.findRelatives.R_test.findRelatives">test.findRelatives: (10 checks) ... OK (48.28 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R">Test file: runit.impute2xxx.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx.R_test.impute2databel">test.impute2databel: (23 checks) ... OK (3.38 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R">Test file: runit.impute2xxx_large.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx_large.R_test.impute2xxx_large">test.impute2xxx_large: (0 checks) ... OK (0.05 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.iterator.R">Test file: runit.iterator.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.iterator.R_test.qtscore">test.qtscore: (0 checks) ... OK (0 seconds)<br/></a></li><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.iterator.R_test.summary_snp_data">test.summary_snp_data: (3 checks) ... OK (38.76 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mach2databel.R">Test file: runit.mach2databel.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.mach2databel.R_test.mach2databel">test.mach2databel: (8 checks) ... OK (1.09 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.merge.R">Test file: runit.merge.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.merge.R_test.merge.bug1641">test.merge.bug1641: (0 checks) ... OK (0.83 seconds)<br/></a></li><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.merge.R_test.merge.bug1676">test.merge.bug1676: (2 checks) ... OK (0.27 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mmscore.R">Test file: runit.mmscore.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.mmscore.R_test.exports">test.exports: (1 checks) ... OK (4.09 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polygenic.R">Test file: runit.polygenic.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polygenic.R_test.polygenic.Bug1322">test.polygenic.Bug1322: (2 checks) ... OK (2.54 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polylik.R">Test file: runit.polylik.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polylik.R_test.polylik">test.polylik: (6 checks) ... OK (3.1 seconds)<br/></a></li></ul></li></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.recodeChromosome.R">Test file: runit.recodeChromosome.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.recodeChromosome.R_test.recodeChromosome">test.recodeChromosome: (8 checks) ... OK (0.22 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.sortmap.internal.R">Test file: runit.sortmap.internal.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.sortmap.internal.R_test.sortmap.internal.bug1673">test.sortmap.internal.bug1673: (1 checks) ... OK (0 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.strandModify.R">Test file: runit.strandModify.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.strandModify.R_test.strandModify">test.strandModify: (2 checks) ... OK (0.06 seconds)<br/></a></li></ul></li></ul><hr>
<table border="0" width="80%" >
<tr><th>Name</th>
<th>Value</th>
</tr>
<tr><td>platform</td>
-<td>x86_64-unknown-linux-gnu</td>
+<td>x86_64-apple-darwin11.2.0</td>
</tr>
<tr><td>arch</td>
<td>x86_64</td>
</tr>
<tr><td>os</td>
-<td>linux-gnu</td>
+<td>darwin11.2.0</td>
</tr>
<tr><td>system</td>
-<td>x86_64, linux-gnu</td>
+<td>x86_64, darwin11.2.0</td>
</tr>
<tr><td>status</td>
<td>Under development (unstable)</td>
@@ -87,10 +68,10 @@
<td>R Under development (unstable) (2011-12-04 r57813)</td>
</tr>
<tr><td>host</td>
-<td>debian</td>
+<td>YAMacBookPro.local</td>
</tr>
<tr><td>compiler</td>
-<td>g++</td>
+<td>NA</td>
</tr>
</table>
</body>
Modified: pkg/GenABEL/inst/unitTests/report.txt
===================================================================
--- pkg/GenABEL/inst/unitTests/report.txt 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/inst/unitTests/report.txt 2012-01-11 18:39:37 UTC (rev 837)
@@ -1,15 +1,12 @@
-RUNIT TEST PROTOCOL -- Tue Dec 6 13:20:55 2011
+RUNIT TEST PROTOCOL -- Wed Jan 11 19:21:05 2012
***********************************************
Number of test functions: 18
Number of errors: 0
-Number of failures: 2
+Number of failures: 0
1 Test Suite :
-GenABEL unit testing - 18 test functions, 0 errors, 2 failures
-FAILURE in test.exports: Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
-FAILURE in test.polylik: Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
- Mean relative difference: 1.756053e-08
+GenABEL unit testing - 18 test functions, 0 errors, 0 failures
@@ -19,57 +16,54 @@
Test function regexp: ^test.+
Test file regexp: ^runit.+\.[rR]$
Involved directory:
-/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests
+/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R
-test.convert.snp.ped: (0 checks) ... OK (0.12 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R
+test.convert.snp: (4 checks) ... OK (1.43 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R
-test.convert.snp: (4 checks) ... OK (1.49 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R
+test.convert.snp.ped: (0 checks) ... OK (0.02 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R
-test.descriptives.trait: (1 checks) ... OK (0.43 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R
+test.descriptives.trait: (1 checks) ... OK (0.47 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R
-test.exports: FAILURE !! (check number 8)
-Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R
+test.exports: (50 checks) ... OK (1.21 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R
-test.findRelatives: (10 checks) ... OK (45.05 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R
+test.findRelatives: (10 checks) ... OK (48.28 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R
-test.impute2xxx_large: (0 checks) ... OK (0.03 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R
+test.impute2databel: (23 checks) ... OK (3.38 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R
-test.impute2databel: (23 checks) ... OK (1.15 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R
+test.impute2xxx_large: (0 checks) ... OK (0.05 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.iterator.R
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.iterator.R
test.qtscore: (0 checks) ... OK (0 seconds)
-test.summary_snp_data: (3 checks) ... OK (8.34 seconds)
+test.summary_snp_data: (3 checks) ... OK (38.76 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mach2databel.R
-test.mach2databel: (8 checks) ... OK (0.97 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mach2databel.R
+test.mach2databel: (8 checks) ... OK (1.09 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.merge.R
-test.merge.bug1641: (0 checks) ... OK (0.17 seconds)
-test.merge.bug1676: (2 checks) ... OK (0.2 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.merge.R
+test.merge.bug1641: (0 checks) ... OK (0.83 seconds)
+test.merge.bug1676: (2 checks) ... OK (0.27 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mmscore.R
-test.exports: (1 checks) ... OK (0.65 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mmscore.R
+test.exports: (1 checks) ... OK (4.09 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polygenic.R
-test.polygenic.Bug1322: (2 checks) ... OK (1.05 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polygenic.R
+test.polygenic.Bug1322: (2 checks) ... OK (2.54 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polylik.R
-test.polylik: FAILURE !! (check number 4)
-Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
- Mean relative difference: 1.756053e-08
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polylik.R
+test.polylik: (6 checks) ... OK (3.1 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.recodeChromosome.R
-test.recodeChromosome: (8 checks) ... OK (0.19 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.recodeChromosome.R
+test.recodeChromosome: (8 checks) ... OK (0.22 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.sortmap.internal.R
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.sortmap.internal.R
test.sortmap.internal.bug1673: (1 checks) ... OK (0 seconds)
---------------------------
-Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.strandModify.R
-test.strandModify: (2 checks) ... OK (0.05 seconds)
+Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.strandModify.R
+test.strandModify: (2 checks) ... OK (0.06 seconds)
Modified: pkg/GenABEL/inst/unitTests/reportSummary.txt
===================================================================
--- pkg/GenABEL/inst/unitTests/reportSummary.txt 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/inst/unitTests/reportSummary.txt 2012-01-11 18:39:37 UTC (rev 837)
@@ -1,12 +1,9 @@
-RUNIT TEST PROTOCOL -- Tue Dec 6 13:20:55 2011
+RUNIT TEST PROTOCOL -- Wed Jan 11 19:21:05 2012
***********************************************
Number of test functions: 18
Number of errors: 0
-Number of failures: 2
+Number of failures: 0
1 Test Suite :
-GenABEL unit testing - 18 test functions, 0 errors, 2 failures
-FAILURE in test.exports: Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
-FAILURE in test.polylik: Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
- Mean relative difference: 1.756053e-08
+GenABEL unit testing - 18 test functions, 0 errors, 0 failures
Modified: pkg/GenABEL/man/ibs.Rd
===================================================================
--- pkg/GenABEL/man/ibs.Rd 2012-01-11 16:08:06 UTC (rev 836)
+++ pkg/GenABEL/man/ibs.Rd 2012-01-11 18:39:37 UTC (rev 837)
@@ -1,72 +1,60 @@
\name{ibs}
\alias{ibs}
-\title{Computes (average) Idenity-by-State for a set of people and markers}
-\description{
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 837
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