diff -Nru r-cran-genetics-1.3.8/debian/changelog r-cran-genetics-1.3.8.1/debian/changelog
--- r-cran-genetics-1.3.8/debian/changelog	2013-05-01 00:38:25.000000000 +0000
+++ r-cran-genetics-1.3.8.1/debian/changelog	2014-06-28 06:41:44.000000000 +0000
@@ -1,3 +1,11 @@
+r-cran-genetics (1.3.8.1-1) unstable; urgency=medium
+
+  * New upstream release
+  * cme fix dpkg-control
+  * add autopkgtest
+
+ -- Andreas Tille <tille@debian.org>  Sat, 28 Jun 2014 08:37:29 +0200
+
 r-cran-genetics (1.3.8-1) unstable; urgency=low
 
   * New upstream release.
diff -Nru r-cran-genetics-1.3.8/debian/control r-cran-genetics-1.3.8.1/debian/control
--- r-cran-genetics-1.3.8/debian/control	2013-05-01 00:36:19.000000000 +0000
+++ r-cran-genetics-1.3.8.1/debian/control	2014-06-28 06:40:04.000000000 +0000
@@ -5,6 +5,7 @@
            Andreas Tille <tille@debian.org>
 Section: gnu-r
 Priority: optional
+Testsuite: autopkgtest
 Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,
@@ -13,7 +14,7 @@
                r-cran-gdata,
                r-cran-gtools,
                r-cran-mass
-Standards-Version: 3.9.4
+Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genetics/trunk/ 
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genetics/trunk/
 Homepage: http://cran.r-project.org/web/packages/genetics
@@ -43,4 +44,3 @@
  The R-Genetics project has developed an set of enhanced genetics
  packages to replace 'genetics'. Please visit the project homepage
  at http://rgenetics.org for information.
-
diff -Nru r-cran-genetics-1.3.8/debian/docs r-cran-genetics-1.3.8.1/debian/docs
--- r-cran-genetics-1.3.8/debian/docs	2011-06-29 14:35:14.000000000 +0000
+++ r-cran-genetics-1.3.8.1/debian/docs	2014-06-27 19:23:05.000000000 +0000
@@ -1 +1,3 @@
 tests
+debian/README.test
+debian/tests/run-unit-test
diff -Nru r-cran-genetics-1.3.8/debian/README.test r-cran-genetics-1.3.8.1/debian/README.test
--- r-cran-genetics-1.3.8/debian/README.test	2011-06-29 14:35:14.000000000 +0000
+++ r-cran-genetics-1.3.8.1/debian/README.test	2014-06-28 06:20:42.000000000 +0000
@@ -1,2 +1,10 @@
-After installing this package, you can test it with the commands in the
-directory “/usr/share/doc/r-cran-genetics/tests”.
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests provided by the package you can do
+
+   sh  run-unit-test
+
+in this directory.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 27 Jun 2014 19:02:17 +0200
diff -Nru r-cran-genetics-1.3.8/debian/tests/control r-cran-genetics-1.3.8.1/debian/tests/control
--- r-cran-genetics-1.3.8/debian/tests/control	1970-01-01 00:00:00.000000000 +0000
+++ r-cran-genetics-1.3.8.1/debian/tests/control	2014-06-27 19:05:30.000000000 +0000
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff -Nru r-cran-genetics-1.3.8/debian/tests/run-unit-test r-cran-genetics-1.3.8.1/debian/tests/run-unit-test
--- r-cran-genetics-1.3.8/debian/tests/run-unit-test	1970-01-01 00:00:00.000000000 +0000
+++ r-cran-genetics-1.3.8.1/debian/tests/run-unit-test	2014-06-28 06:48:19.000000000 +0000
@@ -0,0 +1,22 @@
+#!/bin/sh -e
+
+pkg=r-cran-genetics
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+#gunzip *.gz
+export LC_ALL=C
+for test in *R
+do
+  R CMD BATCH ${test}
+  if [ ! $? ] ; then
+    echo "Test ${test} failed"
+    exit 1
+  else
+    echo "Test ${test} passed"
+  fi
+  rm -f ${test}out .RData
+done
+rm -f $ADTTMP/*
diff -Nru r-cran-genetics-1.3.8/DESCRIPTION r-cran-genetics-1.3.8.1/DESCRIPTION
--- r-cran-genetics-1.3.8/DESCRIPTION	2012-12-15 06:32:16.000000000 +0000
+++ r-cran-genetics-1.3.8.1/DESCRIPTION	2013-09-03 10:06:28.000000000 +0000
@@ -1,6 +1,6 @@
 Package: genetics
 Title: Population Genetics
-Version: 1.3.8
+Version: 1.3.8.1
 Date: 2012-11-26
 Author: Gregory Warnes, with contributions from Gregor Gorjanc,
         Friedrich Leisch, and Michael Man.
@@ -15,6 +15,7 @@
         linkage disequilibrium, ...
 biocViews: Genetics
 License: GPL
-Packaged: 2012-12-14 20:31:44 UTC; warnegr1
+Packaged: 2013-09-03 10:04:45 UTC; ripley
 Repository: CRAN
-Date/Publication: 2012-12-15 07:32:16
+Date/Publication: 2013-09-03 12:06:28
+NeedsCompilation: no
diff -Nru r-cran-genetics-1.3.8/examples/Allele_Freq.out r-cran-genetics-1.3.8.1/examples/Allele_Freq.out
--- r-cran-genetics-1.3.8/examples/Allele_Freq.out	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/Allele_Freq.out	1970-01-01 00:00:00.000000000 +0000
@@ -1,66 +0,0 @@
-Warning message: 
-Unable to read input file name from the environment
-variable '$ALLELE_INPUT_FILENAME'. Using 'input.data.txt' instead.
- 
-
-Reading data file 'test.data.txt' ...
-99  rows and  4  columns were read. 
-
-Column names are:  Patient.ID Locus Marker Genotype 
-Note: Spaces and '<-' characters are converted to periods ('.') 
-
-+-------------------------------------
-|	Gene:	  P53 
-|	Marker:	  C1556G 
-+-------------------------------------
-
-Allele Frequency:
-   Count Proportion
-C      6  0.0909091
-G     60  0.9090909
-NA     0         NA
-
-Genotype Frequency:
-    Count Proportion
-G/C     6  0.1818182
-G/G    27  0.8181818
-NA      0         NA
-
-
-+-------------------------------------
-|	Gene:	  P53 
-|	Marker:	  T127A 
-+-------------------------------------
-
-Allele Frequency:
-   Count Proportion
-A     46  0.6969697
-T     20  0.3030303
-NA     0         NA
-
-Genotype Frequency:
-    Count Proportion
-A/A    17  0.5151515
-A/T    12  0.3636364
-T/T     4  0.1212121
-NA      0         NA
-
-
-+-------------------------------------
-|	Gene:	  P53 
-|	Marker:	  T5094A 
-+-------------------------------------
-
-Allele Frequency:
-   Count Proportion
-A     56  0.8484848
-T     10  0.1515152
-NA     0         NA
-
-Genotype Frequency:
-    Count Proportion
-A/A    23  0.6969697
-A/T    10  0.3030303
-NA      0         NA
-
-
diff -Nru r-cran-genetics-1.3.8/examples/Allele_Freq.R r-cran-genetics-1.3.8.1/examples/Allele_Freq.R
--- r-cran-genetics-1.3.8/examples/Allele_Freq.R	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/Allele_Freq.R	1970-01-01 00:00:00.000000000 +0000
@@ -1,164 +0,0 @@
-# $Id: Allele_Freq.R 7 2001-05-07 13:22:40Z warnes $
-#
-# $Log$
-# Revision 1.1  2001/05/07 13:22:39  warnes
-# Added example files, code, and output.
-#
-# Revision 1.6  2001/05/01 14:33:17  warneg
-#
-# Updated files to use changed PG database output format.  The new format is
-#
-#    Patient ID,Gene,Marker,Allele1/Allele2
-#
-# Before it was
-#
-#    Patient ID,Gene,Marker,Count of Allele1,Count of Allele2,Count of Allele 3, ...
-#
-# This involved changes in  Allele_Freq.R, HWE_Test.R, and test.data.txt
-#
-# ---
-#
-# Modified Examples.R to remove random values.  This will allow
-# diffing current and previous versions of the code to check for
-# regressions.
-#
-# ---
-#
-# Fixed as.genotype.allele.count() to handle conversions both when when NA values
-# are and are not obtained.
-#
-# Simplified the class type of HWE.test results to "HWE.test" from
-# "HWE.test.allele.freq".
-#
-# Revision 1.5  2001/04/25 17:48:35  warneg
-# Changed to store computed allele and genotype frequencies in a variable before printing them out.
-#
-# Revision 1.4  2001/04/23 19:38:20  warneg
-# Updated to use revised Genomics.R code that provides "genotype" and "haplotype" classes.
-#
-# Revision 1.1  2001/02/06 23:09:44  warneg
-#
-#
-# HWE_Test.R performs the Hardy-Weinberg equilibrium test for the markers
-# supplied in the input file.  Initial revision.
-#
-# Revision 1.2  2001/02/06 17:00:26  warneg
-#
-#
-# Added CVS tags to track version.
-#
-#
-# run as
-#   /usr/local/bin/R --vanilla --slave < Allele<-Freq.R
-
-# first, get the library functions
-source("Genomics.R")  
-# later this will become :
-# library(genomics)
-
-
-# get the name of the file containing the allele data
-file.name <- Sys.getenv("ALLELE_INPUT_FILENAME")
-if(file.name=="")
-  {
-  warning(paste("Unable to read input file name from the environment\n",
-                "variable '\$ALLELE_INPUT_FILENAME'. ", 
-                "Using 'input.data.txt' instead.\n",sep=""));
-  file.name <- "test.data.txt"
-  }
-
-# get the data
-cat("\nReading data file '", file.name, "' ...", "\n", sep="" )
-input.data <- read.table(file.name,sep=", ", header=T)
-
-# report on what we have
-cat( dim(input.data)[1], " rows and ", dim(input.data)[2], " columns were read. \n\n")
-
-cat("Column names are: ", names(input.data), "\n" )
-cat("Note: Spaces and '<-' characters are converted to periods ('.') \n")
-
-# make all names uppercase
-names(input.data) <- toupper(names(input.data)) 
-
-# check that we have "PATIENT.ID", "LOCUS", and "MARKER" fields.
-# If not give warning and assume these are columns 1, 2, and 3.
-if( is.na(match("PATIENT.ID", names(input.data) ) ) )
-{
-	warning(paste( "No column labeled 'PATIENT ID'.\n",
-                       "Assuming that the first column ('",
-                       names(input.data)[1],
-                       "' contains patient id. \n", sep='') ) 
-		
-	names(input.data)[1] <- "PATIENT.ID"
-}
-
-
-
-if( is.na(match("LOCUS", names(input.data) ) ) )
-{
-	warning(paste( "No column labeled 'LOCUS'.\n",
-                       "Assuming that the second column ('",
-                       names(input.data)[2],
-                       "' contains locus/gene name. \n", sep='')) 
-		
-	names(input.data)[2] <- "LOCUS"
-}
-if( is.na(match("MARKER", names(input.data) ) ) )
-{
-	warning(paste( "No column labeled 'MARKER'.",
-                       "Assuming that the third column ('",
-                       names(input.data)[3],
-                       "' contains marker name. \n", sep='')) 
-		
-	names(input.data)[3] <- "MARKER"
-}
-
-if( is.na(match("GENOTYPE", names(input.data) ) ) )
-{
-	warning(paste( "No column labeled 'GENOTYPE'.",
-                       "Assuming that the fourth column ('",
-                       names(input.data)[4],
-                       "' contains genotype. \n", sep='')) 
-		
-	names(input.data)[4] <- "GENOTYPE"
-}
-
-#
-# convert data to 1 record per patient
-#
-
-input.data$LOCUS.MARKER  <-  interaction(input.data$LOCUS,input.data$MARKER)
-
-data  <- unstack( input.data, GENOTYPE ~ LOCUS.MARKER)
-data  <- sapply(data, as.genotype, simplify=F)
-data  <- as.data.frame(data)
-
-## Now iterate through doing the HWE test and displaying output
-
-ind  <- !duplicated(input.data$LOCUS.MARKER)
-namemat  <- input.data[ind,c("LOCUS","MARKER","LOCUS.MARKER")]
-nmarker <-  sum(ind)
-
-for(i in 1:nmarker)
-{
-  gene  <- as.character(namemat[i,"LOCUS"])
-  marker  <- as.character(namemat[i,"MARKER"])
-
-  cat("\n")
-  cat("+-------------------------------------\n");
-  if(!is.null(gene))
-    cat("|\tGene:\t ", gene, "\n");
-  
-  if(!is.null(marker))
-    cat("|\tMarker:\t ", marker, "\n");
-  cat("+-------------------------------------\n");
-
-  # compute and print the allele and genotype frequencies
-  sum  <-  summary(data[,i])
-  print(sum)
-
-  # now do and print the HWE test
-  #hwe  <- HWE.test(sum)
-  #print(hwe)
-}
-
diff -Nru r-cran-genetics-1.3.8/examples/Examples.new r-cran-genetics-1.3.8.1/examples/Examples.new
--- r-cran-genetics-1.3.8/examples/Examples.new	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/Examples.new	1970-01-01 00:00:00.000000000 +0000
@@ -1,382 +0,0 @@
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
- [1] "C/C" "C/T" "C/C" "T/T" "C/C" "C/C" "C/C" "C/C" "T/T" "NA" 
-Alleles: C T 
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
-
-Allele Frequency:
-   Count Proportion
-D     13       0.72
-I      5       0.28
-NA     2         NA
-
-Genotype Frequency:
-    Count Proportion
-D/D     6       0.67
-D/I     1       0.11
-I/I     2       0.22
-NA      1         NA
-
-
-Allele Frequency:
-   Count Proportion
-D     13       0.72
-I      5       0.28
-NA     2         NA
-
-Genotype Frequency:
-    Count Proportion
-D/D     6       0.67
-D/I     1       0.11
-I/I     2       0.22
-NA      1         NA
-
-    g1       g2       g3       g4   
- D/D :6   C/C :6   D/D :6   D/D :6  
- D/I :1   C/T :1   D/I :1   D/I :1  
- I/I :2   T/T :2   I/I :2   I/I :2  
- NA's:1   NA's:1   NA's:1   NA's:1  
-Allele Count (I allele):
- [1]  0  1  0  2  0  0  0  0  2 NA
-Allele Counts:
-       D  I
- [1,]  2  0
- [2,]  1  1
- [3,]  2  0
- [4,]  0  2
- [5,]  2  0
- [6,]  2  0
- [7,]  2  0
- [8,]  2  0
- [9,]  0  2
-[10,] NA NA
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
-[1] TRUE TRUE TRUE
-[1]  TRUE FALSE FALSE
-[1] TRUE TRUE TRUE
-
-Test for Hardy-Wienburg-Equilibrium
-
-Call: 
-HWE.test.genotype(x = test4)
-
-Disequlibrium Estimate:
-D-hat=-0.1111111
-
-Significance Tests:
-           test.stat   p-value lower 95% CI upper 95% CI
-z         -0.5773503 0.5637029   -0.3625792     0.140357
-chisq      0.7500000 0.3864762           NA           NA
-chisq-adj  0.1250000 0.7236736           NA           NA
-
-
-
-Call:
-lm(formula = w ~ allele.count(sg, "C"))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--2.3480 -0.7980  0.0920  0.6635  2.4335 
-
-Coefficients:
-                      Estimate Std. Error t value Pr(>|t|)    
-(Intercept)             1.1780     0.2735   4.308  9.4e-05 ***
-allele.count(sg, "C")  -0.0015     0.2368  -0.006    0.995    
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 1.171 on 43 degrees of freedom
-Multiple R-Squared: 9.329e-07,	Adjusted R-squared: -0.02325 
-F-statistic: 4.012e-05 on 1 and 43 degrees of freedom,	p-value: 0.995 
-
-
-Call:
-lm(formula = w ~ allele.ind(sg, "C") + allele.ind(sg, "T"))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--2.0393 -0.6995  0.1805  0.6005  2.1707 
-
-Coefficients:
-                    Estimate Std. Error t value Pr(>|t|)  
-(Intercept)         -0.05817    0.51339  -0.113   0.9103  
-allele.ind(sg, "C")  0.77017    0.37673   2.044   0.0472 *
-allele.ind(sg, "T")  0.92750    0.42717   2.171   0.0356 *
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 1.103 on 42 degrees of freedom
-Multiple R-Squared: 0.1333,	Adjusted R-squared: 0.09206 
-F-statistic: 3.231 on 2 and 42 degrees of freedom,	p-value: 0.04954 
-
-Response Other :
-
-Call:
-lm(formula = Other ~ mg)
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0517 -0.3694 -0.0625  0.3656  1.5183 
-
-Coefficients:
-              Estimate Std. Error t value Pr(>|t|)  
-(Intercept)     0.1650     0.2841   0.581   0.5714  
-mgD/I           0.5050     0.7517   0.672   0.5135  
-mgI/I          -0.7125     0.4492  -1.586   0.1368  
-mgOther/I       1.9050     0.7517   2.534   0.0249 *
-mgOther/Other   0.9367     0.4018   2.331   0.0365 *
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.696 on 13 degrees of freedom
-Multiple R-Squared: 0.6061,	Adjusted R-squared: 0.4849 
-F-statistic:     5 on 4 and 13 degrees of freedom,	p-value: 0.01158 
-
-
-Response D :
-
-Call:
-lm(formula = D ~ mg)
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0517 -0.3694 -0.0625  0.3656  1.5183 
-
-Coefficients:
-              Estimate Std. Error t value Pr(>|t|)   
-(Intercept)     1.1650     0.2841   4.100  0.00125 **
-mgD/I           0.5050     0.7517   0.672  0.51348   
-mgI/I          -1.7125     0.4492  -3.812  0.00216 **
-mgOther/I      -0.0950     0.7517  -0.126  0.90137   
-mgOther/Other  -1.0633     0.4018  -2.646  0.02015 * 
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.696 on 13 degrees of freedom
-Multiple R-Squared: 0.6051,	Adjusted R-squared: 0.4836 
-F-statistic:  4.98 on 4 and 13 degrees of freedom,	p-value: 0.01176 
-
-
-Response I :
-
-Call:
-lm(formula = I ~ mg)
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0517 -0.3694 -0.0625  0.3656  1.5183 
-
-Coefficients:
-              Estimate Std. Error t value Pr(>|t|)  
-(Intercept)    0.16500    0.28413   0.581   0.5714  
-mgD/I          1.50500    0.75172   2.002   0.0666 .
-mgI/I          0.28750    0.44924   0.640   0.5333  
-mgOther/I      1.90500    0.75172   2.534   0.0249 *
-mgOther/Other -0.06333    0.40181  -0.158   0.8772  
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.696 on 13 degrees of freedom
-Multiple R-Squared: 0.456,	Adjusted R-squared: 0.2886 
-F-statistic: 2.724 on 4 and 13 degrees of freedom,	p-value: 0.07578 
-
-
-[1] "Other" "D"     "I"    
-Response Other :
-
-Call:
-lm(formula = Other ~ allele.count(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.1837 -0.5711 -0.0847  0.3322  1.5847 
-
-Coefficients: (1 not defined because of singularities)
-                      Estimate Std. Error t value Pr(>|t|)  
-(Intercept)            -0.2631     0.3806  -0.691   0.4999  
-allele.count(mg)Other   0.7484     0.2552   2.933   0.0103 *
-allele.count(mg)D       0.2428     0.2552   0.952   0.3564  
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.8055 on 15 degrees of freedom
-Multiple R-Squared: 0.3911,	Adjusted R-squared:  0.31 
-F-statistic: 4.818 on 2 and 15 degrees of freedom,	p-value: 0.0242 
-
-
-Response D :
-
-Call:
-lm(formula = D ~ allele.count(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.1437 -0.5611 -0.1047  0.3122  1.4263 
-
-Coefficients: (1 not defined because of singularities)
-                      Estimate Std. Error t value Pr(>|t|)   
-(Intercept)            -0.2631     0.3724  -0.707  0.49064   
-allele.count(mg)Other   0.2284     0.2497   0.915  0.37474   
-allele.count(mg)D       0.7628     0.2497   3.055  0.00802 **
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.7882 on 15 degrees of freedom
-Multiple R-Squared: 0.4156,	Adjusted R-squared: 0.3377 
-F-statistic: 5.334 on 2 and 15 degrees of freedom,	p-value: 0.0178 
-
-
-Response I :
-
-Call:
-lm(formula = I ~ allele.count(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.1816 -0.6107 -0.1304  0.3043  1.5590 
-
-Coefficients: (1 not defined because of singularities)
-                      Estimate Std. Error t value Pr(>|t|)  
-(Intercept)             0.7904     0.3981   1.986   0.0657 .
-allele.count(mg)Other  -0.2794     0.2669  -1.047   0.3118  
-allele.count(mg)D      -0.2650     0.2669  -0.993   0.3365  
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.8426 on 15 degrees of freedom
-Multiple R-Squared: 0.0799,	Adjusted R-squared: -0.04278 
-F-statistic: 0.6513 on 2 and 15 degrees of freedom,	p-value: 0.5355 
-
-
-[1] "Other" "D"     "I"    
-Response Other :
-
-Call:
-lm(formula = Other ~ allele.ind(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0848 -0.3942 -0.1069  0.3408  1.4852 
-
-Coefficients:
-                    Estimate Std. Error t value Pr(>|t|)   
-(Intercept)          -1.2842     0.6167  -2.082  0.05613 . 
-allele.ind(mg)Other   2.4189     0.6122   3.951  0.00145 **
-allele.ind(mg)D       1.4161     0.6122   2.313  0.03645 * 
-allele.ind(mg)I       0.7367     0.5159   1.428  0.17527   
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.6755 on 14 degrees of freedom
-Multiple R-Squared: 0.6003,	Adjusted R-squared: 0.5147 
-F-statistic: 7.009 on 3 and 14 degrees of freedom,	p-value: 0.004126 
-
-
-Response D :
-
-Call:
-lm(formula = D ~ allele.ind(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0848 -0.3942 -0.1069  0.3408  1.4852 
-
-Coefficients:
-                    Estimate Std. Error t value Pr(>|t|)   
-(Intercept)          -1.2842     0.6167  -2.082  0.05613 . 
-allele.ind(mg)Other   1.4189     0.6122   2.318  0.03613 * 
-allele.ind(mg)D       2.4161     0.6122   3.946  0.00146 **
-allele.ind(mg)I       0.7367     0.5159   1.428  0.17527   
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.6755 on 14 degrees of freedom
-Multiple R-Squared: 0.5993,	Adjusted R-squared: 0.5135 
-F-statistic:  6.98 on 3 and 14 degrees of freedom,	p-value: 0.004196 
-
-
-Response I :
-
-Call:
-lm(formula = I ~ allele.ind(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0848 -0.3942 -0.1069  0.3408  1.4852 
-
-Coefficients:
-                    Estimate Std. Error t value Pr(>|t|)   
-(Intercept)          -1.2842     0.6167  -2.082  0.05613 . 
-allele.ind(mg)Other   1.4189     0.6122   2.318  0.03613 * 
-allele.ind(mg)D       1.4161     0.6122   2.313  0.03645 * 
-allele.ind(mg)I       1.7367     0.5159   3.366  0.00461 **
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.6755 on 14 degrees of freedom
-Multiple R-Squared: 0.448,	Adjusted R-squared: 0.3298 
-F-statistic: 3.788 on 3 and 14 degrees of freedom,	p-value: 0.0352 
-
-
- [1] "DD/DD" "DD/I"  "DD/DD" "I/I"   "DD/DD" "DD/DD" "DD/DD" "DD/DD" "I/I"  
-[10] "NA"    "I/NA" 
-Alleles: DD I 
-
-Allele Frequency:
-   Count Proportion
-DD    13       0.68
-I      6       0.32
-NA     3         NA
-
-Genotype Frequency:
-      Count Proportion
-DD/DD     6        0.6
-DD/I      1        0.1
-I/I       2        0.2
-I/NA      1        0.1
-NA        1         NA
-
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "I/I"  "NA"  
-[11] "I/NA"
-Alleles: D I 
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "I/I"  "NA"  
-[11] "NA"   "I/NA"
-Alleles: D I 
-
-Allele Frequency:
-   Count Proportion
-DD    13       0.68
-I      6       0.32
-NA     3         NA
-
-Genotype Frequency:
-      Count Proportion
-DD/DD     6        0.6
-DD/I      1        0.1
-I/I       2        0.2
-I/NA      1        0.1
-NA        1         NA
-
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "I/I"  "NA"  
-[11] "I/NA"
-Alleles: D I 
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "I/I"  "NA"  
-[11] "NA/I"
-Alleles: D I 
- [1] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE    NA    NA
- [1]  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE    NA    NA
- [1]  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE    NA    NA
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "D/D"  "D/I" 
-[11] "I/NA"
-Alleles: D I 
-[1] "D/D" "D/I"
-Alleles: D I 
-[1] "D" "D"
-[1] "D" "D"
-
diff -Nru r-cran-genetics-1.3.8/examples/Examples.out r-cran-genetics-1.3.8.1/examples/Examples.out
--- r-cran-genetics-1.3.8/examples/Examples.out	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/Examples.out	1970-01-01 00:00:00.000000000 +0000
@@ -1,382 +0,0 @@
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
- [1] "C/C" "C/T" "C/C" "T/T" "C/C" "C/C" "C/C" "C/C" "T/T" "NA" 
-Alleles: C T 
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
-
-Allele Frequency:
-   Count Proportion
-D     13       0.72
-I      5       0.28
-NA     2         NA
-
-Genotype Frequency:
-    Count Proportion
-D/D     6       0.67
-D/I     1       0.11
-I/I     2       0.22
-NA      1         NA
-
-
-Allele Frequency:
-   Count Proportion
-D     13       0.72
-I      5       0.28
-NA     2         NA
-
-Genotype Frequency:
-    Count Proportion
-D/D     6       0.67
-D/I     1       0.11
-I/I     2       0.22
-NA      1         NA
-
-    g1       g2       g3       g4   
- D/D :6   C/C :6   D/D :6   D/D :6  
- D/I :1   C/T :1   D/I :1   D/I :1  
- I/I :2   T/T :2   I/I :2   I/I :2  
- NA's:1   NA's:1   NA's:1   NA's:1  
-Allele Count (I allele):
- [1]  0  1  0  2  0  0  0  0  2 NA
-Allele Counts:
-       D  I
- [1,]  2  0
- [2,]  1  1
- [3,]  2  0
- [4,]  0  2
- [5,]  2  0
- [6,]  2  0
- [7,]  2  0
- [8,]  2  0
- [9,]  0  2
-[10,] NA NA
- [1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" "NA" 
-Alleles: D I 
-[1] TRUE TRUE TRUE
-[1]  TRUE FALSE FALSE
-[1] TRUE TRUE TRUE
-
-Test for Hardy-Wienburg-Equilibrium
-
-Call: 
-HWE.test.genotype(x = test4)
-
-Disequlibrium Estimate:
-D-hat=-0.1111111
-
-Significance Tests:
-           test.stat   p-value lower 95% CI upper 95% CI
-z         -0.5773503 0.5637029   -0.3625792     0.140357
-chisq      0.7500000 0.3864762           NA           NA
-chisq-adj  0.1250000 0.7236736           NA           NA
-
-
-
-Call:
-lm(formula = w ~ allele.count(sg, "C"))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--2.3480 -0.7980  0.0920  0.6635  2.4335 
-
-Coefficients:
-                      Estimate Std. Error t value Pr(>|t|)    
-(Intercept)             1.1780     0.2735   4.308  9.4e-05 ***
-allele.count(sg, "C")  -0.0015     0.2368  -0.006    0.995    
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 1.171 on 43 degrees of freedom
-Multiple R-Squared: 9.329e-07,	Adjusted R-squared: -0.02325 
-F-statistic: 4.012e-05 on 1 and 43 degrees of freedom,	p-value: 0.995 
-
-
-Call:
-lm(formula = w ~ allele.ind(sg, "C") + allele.ind(sg, "T"))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--2.0393 -0.6995  0.1805  0.6005  2.1707 
-
-Coefficients:
-                    Estimate Std. Error t value Pr(>|t|)  
-(Intercept)         -0.05817    0.51339  -0.113   0.9103  
-allele.ind(sg, "C")  0.77017    0.37673   2.044   0.0472 *
-allele.ind(sg, "T")  0.92750    0.42717   2.171   0.0356 *
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 1.103 on 42 degrees of freedom
-Multiple R-Squared: 0.1333,	Adjusted R-squared: 0.09206 
-F-statistic: 3.231 on 2 and 42 degrees of freedom,	p-value: 0.04954 
-
-Response Other :
-
-Call:
-lm(formula = Other ~ mg)
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0517 -0.3694 -0.0625  0.3656  1.5183 
-
-Coefficients:
-              Estimate Std. Error t value Pr(>|t|)  
-(Intercept)     0.1650     0.2841   0.581   0.5714  
-mgD/I           0.5050     0.7517   0.672   0.5135  
-mgI/I          -0.7125     0.4492  -1.586   0.1368  
-mgOther/I       1.9050     0.7517   2.534   0.0249 *
-mgOther/Other   0.9367     0.4018   2.331   0.0365 *
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.696 on 13 degrees of freedom
-Multiple R-Squared: 0.6061,	Adjusted R-squared: 0.4849 
-F-statistic:     5 on 4 and 13 degrees of freedom,	p-value: 0.01158 
-
-
-Response D :
-
-Call:
-lm(formula = D ~ mg)
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0517 -0.3694 -0.0625  0.3656  1.5183 
-
-Coefficients:
-              Estimate Std. Error t value Pr(>|t|)   
-(Intercept)     1.1650     0.2841   4.100  0.00125 **
-mgD/I           0.5050     0.7517   0.672  0.51348   
-mgI/I          -1.7125     0.4492  -3.812  0.00216 **
-mgOther/I      -0.0950     0.7517  -0.126  0.90137   
-mgOther/Other  -1.0633     0.4018  -2.646  0.02015 * 
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.696 on 13 degrees of freedom
-Multiple R-Squared: 0.6051,	Adjusted R-squared: 0.4836 
-F-statistic:  4.98 on 4 and 13 degrees of freedom,	p-value: 0.01176 
-
-
-Response I :
-
-Call:
-lm(formula = I ~ mg)
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0517 -0.3694 -0.0625  0.3656  1.5183 
-
-Coefficients:
-              Estimate Std. Error t value Pr(>|t|)  
-(Intercept)    0.16500    0.28413   0.581   0.5714  
-mgD/I          1.50500    0.75172   2.002   0.0666 .
-mgI/I          0.28750    0.44924   0.640   0.5333  
-mgOther/I      1.90500    0.75172   2.534   0.0249 *
-mgOther/Other -0.06333    0.40181  -0.158   0.8772  
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.696 on 13 degrees of freedom
-Multiple R-Squared: 0.456,	Adjusted R-squared: 0.2886 
-F-statistic: 2.724 on 4 and 13 degrees of freedom,	p-value: 0.07578 
-
-
-[1] "Other" "D"     "I"    
-Response Other :
-
-Call:
-lm(formula = Other ~ allele.count(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.1837 -0.5711 -0.0847  0.3322  1.5847 
-
-Coefficients: (1 not defined because of singularities)
-                      Estimate Std. Error t value Pr(>|t|)  
-(Intercept)            -0.2631     0.3806  -0.691   0.4999  
-allele.count(mg)Other   0.7484     0.2552   2.933   0.0103 *
-allele.count(mg)D       0.2428     0.2552   0.952   0.3564  
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.8055 on 15 degrees of freedom
-Multiple R-Squared: 0.3911,	Adjusted R-squared:  0.31 
-F-statistic: 4.818 on 2 and 15 degrees of freedom,	p-value: 0.0242 
-
-
-Response D :
-
-Call:
-lm(formula = D ~ allele.count(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.1437 -0.5611 -0.1047  0.3122  1.4263 
-
-Coefficients: (1 not defined because of singularities)
-                      Estimate Std. Error t value Pr(>|t|)   
-(Intercept)            -0.2631     0.3724  -0.707  0.49064   
-allele.count(mg)Other   0.2284     0.2497   0.915  0.37474   
-allele.count(mg)D       0.7628     0.2497   3.055  0.00802 **
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.7882 on 15 degrees of freedom
-Multiple R-Squared: 0.4156,	Adjusted R-squared: 0.3377 
-F-statistic: 5.334 on 2 and 15 degrees of freedom,	p-value: 0.0178 
-
-
-Response I :
-
-Call:
-lm(formula = I ~ allele.count(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.1816 -0.6107 -0.1304  0.3043  1.5590 
-
-Coefficients: (1 not defined because of singularities)
-                      Estimate Std. Error t value Pr(>|t|)  
-(Intercept)             0.7904     0.3981   1.986   0.0657 .
-allele.count(mg)Other  -0.2794     0.2669  -1.047   0.3118  
-allele.count(mg)D      -0.2650     0.2669  -0.993   0.3365  
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.8426 on 15 degrees of freedom
-Multiple R-Squared: 0.0799,	Adjusted R-squared: -0.04278 
-F-statistic: 0.6513 on 2 and 15 degrees of freedom,	p-value: 0.5355 
-
-
-[1] "Other" "D"     "I"    
-Response Other :
-
-Call:
-lm(formula = Other ~ allele.ind(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0848 -0.3942 -0.1069  0.3408  1.4852 
-
-Coefficients:
-                    Estimate Std. Error t value Pr(>|t|)   
-(Intercept)          -1.2842     0.6167  -2.082  0.05613 . 
-allele.ind(mg)Other   2.4189     0.6122   3.951  0.00145 **
-allele.ind(mg)D       1.4161     0.6122   2.313  0.03645 * 
-allele.ind(mg)I       0.7367     0.5159   1.428  0.17527   
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.6755 on 14 degrees of freedom
-Multiple R-Squared: 0.6003,	Adjusted R-squared: 0.5147 
-F-statistic: 7.009 on 3 and 14 degrees of freedom,	p-value: 0.004126 
-
-
-Response D :
-
-Call:
-lm(formula = D ~ allele.ind(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0848 -0.3942 -0.1069  0.3408  1.4852 
-
-Coefficients:
-                    Estimate Std. Error t value Pr(>|t|)   
-(Intercept)          -1.2842     0.6167  -2.082  0.05613 . 
-allele.ind(mg)Other   1.4189     0.6122   2.318  0.03613 * 
-allele.ind(mg)D       2.4161     0.6122   3.946  0.00146 **
-allele.ind(mg)I       0.7367     0.5159   1.428  0.17527   
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.6755 on 14 degrees of freedom
-Multiple R-Squared: 0.5993,	Adjusted R-squared: 0.5135 
-F-statistic:  6.98 on 3 and 14 degrees of freedom,	p-value: 0.004196 
-
-
-Response I :
-
-Call:
-lm(formula = I ~ allele.ind(mg))
-
-Residuals:
-    Min      1Q  Median      3Q     Max 
--1.0848 -0.3942 -0.1069  0.3408  1.4852 
-
-Coefficients:
-                    Estimate Std. Error t value Pr(>|t|)   
-(Intercept)          -1.2842     0.6167  -2.082  0.05613 . 
-allele.ind(mg)Other   1.4189     0.6122   2.318  0.03613 * 
-allele.ind(mg)D       1.4161     0.6122   2.313  0.03645 * 
-allele.ind(mg)I       1.7367     0.5159   3.366  0.00461 **
----
-Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1  ` '  1 
-
-Residual standard error: 0.6755 on 14 degrees of freedom
-Multiple R-Squared: 0.448,	Adjusted R-squared: 0.3298 
-F-statistic: 3.788 on 3 and 14 degrees of freedom,	p-value: 0.0352 
-
-
- [1] "DD/DD" "DD/I"  "DD/DD" "I/I"   "DD/DD" "DD/DD" "DD/DD" "DD/DD" "I/I"  
-[10] "NA"    "I/NA" 
-Alleles: DD I 
-
-Allele Frequency:
-   Count Proportion
-DD    13       0.68
-I      6       0.32
-NA     3         NA
-
-Genotype Frequency:
-      Count Proportion
-DD/DD     6        0.6
-DD/I      1        0.1
-I/I       2        0.2
-I/NA      1        0.1
-NA        1         NA
-
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "I/I"  "NA"  
-[11] "I/NA"
-Alleles: D I 
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "I/I"  "NA"  
-[11] "NA"   "I/NA"
-Alleles: D I 
-
-Allele Frequency:
-   Count Proportion
-DD    13       0.68
-I      6       0.32
-NA     3         NA
-
-Genotype Frequency:
-      Count Proportion
-DD/DD     6        0.6
-DD/I      1        0.1
-I/I       2        0.2
-I/NA      1        0.1
-NA        1         NA
-
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "I/I"  "NA"  
-[11] "I/NA"
-Alleles: D I 
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "I/I"  "NA"  
-[11] "NA/I"
-Alleles: D I 
- [1] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE    NA    NA
- [1]  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE    NA    NA
- [1]  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE    NA    NA
- [1] "D/D"  "D/I"  "D/D"  "I/I"  "D/D"  "D/D"  "D/D"  "D/D"  "D/D"  "D/I" 
-[11] "I/NA"
-Alleles: D I 
-[1] "D/D" "D/I"
-Alleles: D I 
-[1] "D" "D"
-[1] "D" "D"
-
diff -Nru r-cran-genetics-1.3.8/examples/Gene.examples r-cran-genetics-1.3.8.1/examples/Gene.examples
--- r-cran-genetics-1.3.8/examples/Gene.examples	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/Gene.examples	1970-01-01 00:00:00.000000000 +0000
@@ -1,4 +0,0 @@
-## Examples
-
-g <- gene("P53","17q 1009232cM")
-m <- marker("C-107QT",g,begin=-107,end=-107,type="SNP")
diff -Nru r-cran-genetics-1.3.8/examples/Genomics.examples r-cran-genetics-1.3.8.1/examples/Genomics.examples
--- r-cran-genetics-1.3.8/examples/Genomics.examples	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/Genomics.examples	1970-01-01 00:00:00.000000000 +0000
@@ -1,124 +0,0 @@
-library(genetics)
-
-### demos
-
-
-example.data   <- c("D/D","D/I","D/D","I/I","D/D","D/D","D/D","D/D","I/I","")
-example.data2  <- c("C-C","C-T","C-C","T-T","C-C","C-C","C-C","C-C","T-T","")
-example.data3  <- c("D   /   D","D   /   I","D   /   D","I   /   I",
-                    "D   /   D","D   /   D","D   /   D","D   /   D",
-                    "I   /   I","")
-example.nosep  <- c("DD", "DI", "DD", "II", "DD", "DD", "DD", "DD", "II", "")
-example.split1 <- c("D",  "D",  "D",  "I",  "D",  "D",  "D",  "D",  "I",  "")
-example.split2 <- c("D",  "I",  "D",  "I",  "D",  "D",  "D",  "D",  "I",  "")
-
-g1  <- genotype(example.data)
-g1
-g2  <- genotype(example.data2,sep="-")
-g2
-g3  <- genotype(example.nosep,sep="")
-g3
-g4  <- genotype(example.split1,example.split2)
-g4
-g5  <- genotype(example.data3,rem=T)
-g5
-
-tmp  <-  data.frame(g1,g2,g3,g4)
-
-# show what summary does in a normal context
-summary(g1)
-summary(tmp$g1)
-
-# show what summary does in a data frame context
-summary(tmp)
-
-allele.count(g1,"I")
-
-ac  <- allele.count(g1)
-ac
-as.genotype(ac)
-
-
-test1  <- genotype(c("C/C", "C/T", "T/C"))
-test2  <- genotype(c("C/C", "T/C", "T/C"))
-test3  <- genotype(c("C/C", "C/C", "T/T"))
-test1==test2
-test1==test3
-
-test4  <-  haplotype(as.character(test1))
-test5  <-  haplotype(as.character(test2))
-test6  <-  haplotype(as.character(test3))
-
-test4==test5
-
-HWE.test(test4)
-
-# test use in linear model
-
-sg  <- genotype(rep(c("C/C","T/C","T/T","T/T","T/T","C/C","T/C","T/C","C/T"),5),reorder="freq")
-"y" <- c(-2.02, 1.15, -0.26, 1.34, 2.54, -1.74, -0.23, 0.34, -0.23, 
-         1.29, 2.03, 0.13, -1.67, 1.23, -1.46, -0.28, -0.75, -0.71, 0.17, 
-         -1.52, 0.57, -0.12, 0.81, 0.49, -0.12, 0.43, 0.31, 0.25, 0.69, 
-         1, -0.43, 2.24, -0.87, 0.74, 0.63, -0.32, -0.06, -1.24, -1.45, 
-         0.77, -1.16, 1.07, -0.56, 2.11, 0.32)
-w  <- y + (carrier(sg,"C") + 0.5 *carrier(sg,"T"))
-summary(lm(w ~ allele.count(sg,"C")))
-summary(lm(w ~ carrier(sg,"C") + carrier(sg,"T")))
-
-boxplot(w ~ allele.count(sg,"C"))
-boxplot(w ~ carrier(sg,"C"))
-
-m1  <-  c("D   /   D","D   /   I","D   /   D","I   /   I","D   /   D",
-          "D   /   D","D   /   D","D   /   D","I   /   I","   /   ",
-          "Other   /   Other","Other   /   I",  "Other   /   Other",
-          "I   /   I", "Other   /   Other","Other   /   Other",
-          "Other   /   Other","Other   /   Other", "I   /   I","   /   ")
-
-mg <- genotype(m1)
-my <- c(0.58, 0.67, 0.04, -0.85, 0.01, -0.46, 0.93, -0.11, -1.06, -1.2, 
-          -0.29, 1.07, 0.49, -0.03, 1.62, 0.37, -0.95, -0.63, -0.25, 0.71)
-mw  <- carrier(mg) + my
-
-summary(lm(mw ~ mg))
-colnames(allele.count(mg))
-summary(lm(mw ~ allele.count(mg)))
-colnames(carrier(mg))
-summary(lm(mw ~ carrier(mg)))
-
-
-
-## "Messy" example
-
-m3  <-  c("D D/\t   D D","D\tD/   I",  "D D/   D D","I/   I",
-          "D D/   D D","D D/   D D","D D/   D D","D D/   D D",
-          "I/   I","/   ","/I")
-
-genotype(m3)
-summary(genotype(m3))
-
-m4  <-  c("D D","D I","D D","I I",
-          "D D","D D","D D","D D",
-          "I I","   ","  I")
-
-genotype(m4,sep=1)
-genotype(m4,sep=" ",remove.spaces=F)
-summary(genotype(m3))
-
-m5  <-  c("DD","DI","DD","II",
-          "DD","DD","DD","DD",
-          "II","   "," I")
-genotype(m5,sep=1)
-haplotype(m5,sep=1,remove.spaces=F)
-
-g5  <- genotype(m5,sep="")
-
-heterozygote(g5)
-homozygote(g5)
-carrier(g5,"D")
-
-g5[9:10]  <- haplotype(m4,sep=" ",remove=F)[1:2]
-g5
-
-g5[9:10]
-allele(g5[9:10],1)
-allele(g5,1)[9:10]
diff -Nru r-cran-genetics-1.3.8/examples/HWE_Test.out r-cran-genetics-1.3.8.1/examples/HWE_Test.out
--- r-cran-genetics-1.3.8/examples/HWE_Test.out	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/HWE_Test.out	1970-01-01 00:00:00.000000000 +0000
@@ -1,114 +0,0 @@
-Warning message: 
-Unable to read input file name from the environment
-variable '$ALLELE_INPUT_FILENAME'. Using 'input.data.txt' instead.
- 
-
-Reading data file 'test.data.txt' ...
-99  rows and  4  columns were read. 
-
-Column names are:  Patient.ID Locus Marker Genotype 
-Note: Spaces and '<-' characters are converted to periods ('.') 
-
-+-------------------------------------
-|	Gene:	  P53 
-|	Marker:	  C1556G 
-+-------------------------------------
-
-Allele Frequency:
-   Count Proportion
-C      6  0.0909091
-G     60  0.9090909
-NA     0         NA
-
-Genotype Frequency:
-    Count Proportion
-G/C     6  0.1818182
-G/G    27  0.8181818
-NA      0         NA
-
-
-Test for Hardy-Wienburg-Equilibrium
-
-Call: 
-HWE.test.summary.genotype(x = sum)
-
-Disequlibrium Estimate:
-D-hat=0.1735537
-
-Significance Tests:
-          test.stat      p-value lower 95% CI upper 95% CI
-z          12.15062 5.693194e-34    0.1453560    0.2017514
-chisq     145.53000 0.000000e+00           NA           NA
-chisq-adj 123.19167 0.000000e+00           NA           NA
-
-
-
-+-------------------------------------
-|	Gene:	  P53 
-|	Marker:	  T127A 
-+-------------------------------------
-
-Allele Frequency:
-   Count Proportion
-A     46  0.6969697
-T     20  0.3030303
-NA     0         NA
-
-Genotype Frequency:
-    Count Proportion
-A/A    17  0.5151515
-A/T    12  0.3636364
-T/T     4  0.1212121
-NA      0         NA
-
-
-Test for Hardy-Wienburg-Equilibrium
-
-Call: 
-HWE.test.summary.genotype(x = sum)
-
-Disequlibrium Estimate:
-D-hat=0.02938476
-
-Significance Tests:
-          test.stat   p-value lower 95% CI upper 95% CI
-z         0.8862823 0.3754654  -0.04267604    0.1014456
-chisq     0.6387902 0.4241492           NA           NA
-chisq-adj 0.2351985 0.6276957           NA           NA
-
-
-
-+-------------------------------------
-|	Gene:	  P53 
-|	Marker:	  T5094A 
-+-------------------------------------
-
-Allele Frequency:
-   Count Proportion
-A     56  0.8484848
-T     10  0.1515152
-NA     0         NA
-
-Genotype Frequency:
-    Count Proportion
-A/A    23  0.6969697
-A/T    10  0.3030303
-NA      0         NA
-
-
-Test for Hardy-Wienburg-Equilibrium
-
-Call: 
-HWE.test.summary.genotype(x = sum)
-
-Disequlibrium Estimate:
-D-hat=-0.02295684
-
-Significance Tests:
-          test.stat   p-value lower 95% CI upper 95% CI
-z         -0.938776 0.3478458  -0.06681993   0.02090625
-chisq      1.052296 0.3049789           NA           NA
-chisq-adj  0.211824 0.6453415           NA           NA
-
-
-
diff -Nru r-cran-genetics-1.3.8/examples/HWE_Test.R r-cran-genetics-1.3.8.1/examples/HWE_Test.R
--- r-cran-genetics-1.3.8/examples/HWE_Test.R	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/HWE_Test.R	1970-01-01 00:00:00.000000000 +0000
@@ -1,175 +0,0 @@
-# $Id: HWE_Test.R 61 2002-06-27 18:46:05Z warnesgr $
-#
-# $Log$
-# Revision 1.2  2002/06/27 18:46:05  warnesgr
-# - Allow user to specify parameters for the chisquare test.
-#
-# Revision 1.1  2001/05/07 13:22:39  warnes
-#
-# Added example files, code, and output.
-#
-# Revision 1.4  2001/05/01 14:33:19  warneg
-#
-# Updated files to use changed PG database output format.  The new format is
-#
-#    Patient ID,Gene,Marker,Allele1/Allele2
-#
-# Before it was
-#
-#    Patient ID,Gene,Marker,Count of Allele1,Count of Allele2,Count of Allele 3, ...
-#
-# This involved changes in  Allele_Freq.R, HWE_Test.R, and test.data.txt
-#
-# ---
-#
-# Modified Examples.R to remove random values.  This will allow
-# diffing current and previous versions of the code to check for
-# regressions.
-#
-# ---
-#
-# Fixed as.genotype.allele.count() to handle conversions both when when NA values
-# are and are not obtained.
-#
-# Simplified the class type of HWE.test results to "HWE.test" from
-# "HWE.test.allele.freq".
-#
-# Revision 1.3  2001/04/25 17:45:37  warneg
-# Fixed typo that caused an error.
-#
-# Revision 1.2  2001/04/23 19:39:01  warneg
-# Updated to use revised Genomics.R that provides "genotype" and "haplotype" classes.
-#
-# Revision 1.1  2001/02/06 23:09:44  warneg
-#
-#
-# HWE_Test.R performs the Hardy-Weinberg equilibrium test for the markers
-# supplied in the input file.  Initial revision.
-#
-# Revision 1.2  2001/02/06 17:00:26  warneg
-#
-#
-# Added CVS tags to track version.
-#
-#
-# run as
-#   /usr/local/bin/R --vanilla --slave < Allele<-Freq.R
-
-# first, get the library functions
-library(genetics)
-
-
-# get the name of the file containing the allele data
-file.name <- Sys.getenv("ALLELE_INPUT_FILENAME")
-if(file.name=="")
-  {
-  warning(paste("Unable to read input file name from the environment\n",
-                "variable '\$ALLELE_INPUT_FILENAME'. ", 
-                "Using 'input.data.txt' instead.\n",sep=""));
-  file.name <- "test.data.txt"
-  }
-
-# get the data
-cat("\nReading data file '", file.name, "' ...", "\n", sep="" )
-input.data <- read.table(file.name,sep=", ", header=T)
-
-# report on what we have
-cat( dim(input.data)[1], " rows and ", dim(input.data)[2], " columns were read. \n\n")
-
-cat("Column names are: ", names(input.data), "\n" )
-cat("Note: Spaces and '<-' characters are converted to periods ('.') \n")
-
-# make all names uppercase
-names(input.data) <- toupper(names(input.data)) 
-
-# check that we have "PATIENT.ID", "LOCUS", and "MARKER" fields.
-# If not give warning and assume these are columns 1, 2, and 3.
-if( is.na(match("PATIENT.ID", names(input.data) ) ) )
-{
-	warning(paste( "No column labeled 'PATIENT ID'.\n",
-                       "Assuming that the first column ('",
-                       names(input.data)[1],
-                       "' contains patient id. \n", sep='') ) 
-		
-	names(input.data)[1] <- "PATIENT.ID"
-}
-
-
-
-if( is.na(match("LOCUS", names(input.data) ) ) )
-{
-	warning(paste( "No column labeled 'LOCUS'.\n",
-                       "Assuming that the second column ('",
-                       names(input.data)[2],
-                       "' contains locus/gene name. \n", sep='')) 
-		
-	names(input.data)[2] <- "LOCUS"
-}
-if( is.na(match("MARKER", names(input.data) ) ) )
-{
-	warning(paste( "No column labeled 'MARKER'.",
-                       "Assuming that the third column ('",
-                       names(input.data)[3],
-                       "' contains marker name. \n", sep='')) 
-		
-	names(input.data)[3] <- "MARKER"
-}
-
-if( is.na(match("GENOTYPE", names(input.data) ) ) )
-{
-	warning(paste( "No column labeled 'GENOTYPE'.",
-                       "Assuming that the fourth column ('",
-                       names(input.data)[4],
-                       "' contains genotype. \n", sep='')) 
-		
-	names(input.data)[4] <- "GENOTYPE"
-}
-
-#
-# convert data to 1 record per patient
-#
-input.data$LOCUS.MARKER  <-  paste(input.data$LOCUS,input.data$MARKER,sep=":")
-data  <- data.frame(PATIENT.ID=unique(as.character(input.data$PATIENT.ID)))
-data[,unique(input.data$LOCUS.MARKER)]  <- NA
-data  <- as.matrix(data)
-rownames(data)  <-  data[,1]
-
-tmp  <- split(input.data[,c("PATIENT.ID","LOCUS.MARKER","GENOTYPE")], input.data$LOCUS.MARKER)
-
-for(i in 1:nrow(input.data))
-  data[ as.character(input.data[i,"PATIENT.ID"]), 
-       as.character(input.data[i,"LOCUS.MARKER"]) ]  <-
-  as.character(input.data[i,"GENOTYPE"])
-
-data  <- data.frame(apply( data[,-1], 2, as.character ))
-data  <- data.frame(sapply( data, as.genotype, simplify=F))
-
-## Now iterate through doing the HWE test and displaying output
-
-ind  <- !duplicated(input.data$LOCUS.MARKER)
-namemat  <- input.data[ind,c("LOCUS","MARKER","LOCUS.MARKER")]
-nmarker <-  sum(ind)
-
-for(i in 1:nmarker)
-{
-  gene  <- as.character(namemat[i,"LOCUS"])
-  marker  <- as.character(namemat[i,"MARKER"])
-
-  cat("\n")
-  cat("+-------------------------------------\n");
-  if(!is.null(gene))
-    cat("|\tGene:\t ", gene, "\n");
-  
-  if(!is.null(marker))
-    cat("|\tMarker:\t ", marker, "\n");
-  cat("+-------------------------------------\n");
-
-  # compute and print the allele and genotype frequencies
-  sum  <-  summary(data[,i])
-  print(sum)
-
-  # now do and print the HWE test
-  hwe  <- HWE.test(data[,i])
-  print(hwe)
-}
-
diff -Nru r-cran-genetics-1.3.8/examples/locus.example.R r-cran-genetics-1.3.8.1/examples/locus.example.R
--- r-cran-genetics-1.3.8/examples/locus.example.R	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/locus.example.R	1970-01-01 00:00:00.000000000 +0000
@@ -1,51 +0,0 @@
-
-
-ar2  <- gene("AR2",chromosome=7,arm="q",index.start=35)
-ar2
-
-par  <- locus(name="AR2 Psedogene", 
-              chromosome=1, 
-              arm="q",
-              index.start=32,
-              index.end=42)
-par
-
-c109t  <- marker(name="C-109T",
-                 type="SNP",
-                 locus.name="AR2",
-                 chromosome=7, 
-                 arm="q", 
-                 index.start=35,
-                 bp.start=-109,
-                 relative.to="start of coding region")
-c109t
-
-c109t  <- marker(name="C-109T",
-                 type="SNP",
-                 locus=ar2,
-                 bp.start=-109,
-                 relative.to="start of coding region")
-c109t
-
-
-
-
-example.data   <- c("D/D","D/I","D/D","I/I","D/D","D/D","D/D","D/D","I/I","")
-g1  <- genotype(example.data, locus=ar2)
-g1
-summary(g1)
-HWE.test(g1)
-
-g2  <- genotype(example.data, locus=c109t)
-summary(g2)
-
-getlocus(g2)
-
-heterozygote(g2)
-homozygote(g1)
-
-allele(g1,1)
-
-carrier(g1,"I")
-
-heterozygote(g2)
diff -Nru r-cran-genetics-1.3.8/examples/test.ci.R r-cran-genetics-1.3.8.1/examples/test.ci.R
--- r-cran-genetics-1.3.8/examples/test.ci.R	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/test.ci.R	1970-01-01 00:00:00.000000000 +0000
@@ -1,18 +0,0 @@
-# test 3 allele model
-
-library(genetics)
-library(combinat)
-
-gen3 <- function(d=0, nobs=20)
-  {
-    pvec <- c(aa=1+d, ab=2*(1-d), ac=2*(1-d), bb=1+d, bc=2*(1-d), cc=1+d)
-    pvec <- pvec/sum(pvec)
-
-    gen <- rmultinomial(n=nobs, p=rbind(pvec), rows=1)
-    genotype( rep( c("A/A","A/B","A/C","B/B","B/C","C/C"), gen), alleles=c("A","B","C") )
-  }
-
-worker <- function(...)
-  diseq.ci(gen3())$ci
-
-sim <- t(sapply(1:10, function(x) worker))
diff -Nru r-cran-genetics-1.3.8/examples/test.data.2.txt r-cran-genetics-1.3.8.1/examples/test.data.2.txt
--- r-cran-genetics-1.3.8/examples/test.data.2.txt	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/test.data.2.txt	1970-01-01 00:00:00.000000000 +0000
@@ -1,515 +0,0 @@
-Patient Id,Locus,Marker,Genotype
-1214,IL-1 beta,C3953T,C/T
-1214,IL-1 beta,T-31C,T/C
-1175,IL-1 beta,C-511T,C/C
-1175,IL-1 beta,T-31C,T/T
-1175,IL-1 beta,C3953T,C/C
-1175,IL1RN,IL1RN-VNTR,1/1
-1176,IL-1 beta,C-511T,T/T
-1176,IL-1 beta,T-31C,C/C
-1176,IL-1 beta,C3953T,C/C
-1176,IL1RN,IL1RN-VNTR,1/1
-1177,IL-1 beta,C-511T,C/T
-1177,IL-1 beta,T-31C,T/C
-1177,IL-1 beta,C3953T,C/C
-1177,IL1RN,IL1RN-VNTR,1/2
-1178,IL-1 beta,C-511T,T/T
-1178,IL-1 beta,T-31C,C/C
-1178,IL-1 beta,C3953T,C/C
-1178,IL1RN,IL1RN-VNTR,1/2
-1179,IL-1 beta,C-511T,C/C
-1179,IL-1 beta,T-31C,T/T
-1179,IL-1 beta,C3953T,C/C
-1179,IL1RN,IL1RN-VNTR,1/1
-1180,IL-1 beta,C-511T,C/C
-1180,IL-1 beta,T-31C,T/T
-1180,IL-1 beta,C3953T,C/C
-1180,IL1RN,IL1RN-VNTR,1/1
-1165,IL-1 beta,C-511T,T/T
-1165,IL-1 beta,T-31C,C/C
-1165,IL-1 beta,C3953T,C/C
-1165,IL1RN,IL1RN-VNTR,1/1
-1092,IL-1 beta,C-511T,C/T
-1092,IL-1 beta,T-31C,T/C
-1092,IL-1 beta,C3953T,C/C
-1092,IL1RN,IL1RN-VNTR,1/1
-1198,IL-1 beta,C-511T,C/T
-1198,IL-1 beta,T-31C,T/C
-1198,IL-1 beta,C3953T,C/C
-1198,IL1RN,IL1RN-VNTR,1/1
-1199,IL-1 beta,C-511T,C/T
-1199,IL-1 beta,T-31C,T/C
-1199,IL-1 beta,C3953T,C/C
-1199,IL1RN,IL1RN-VNTR,2/2
-1200,IL-1 beta,C-511T,C/T
-1200,IL-1 beta,T-31C,T/C
-1200,IL-1 beta,C3953T,C/C
-1200,IL1RN,IL1RN-VNTR,1/2
-1201,IL-1 beta,C-511T,C/T
-1201,IL-1 beta,T-31C,T/C
-1201,IL-1 beta,C3953T,T/T
-1201,IL1RN,IL1RN-VNTR,1/1
-1202,IL-1 beta,C-511T,T/T
-1202,IL-1 beta,T-31C,C/C
-1202,IL-1 beta,C3953T,C/C
-1202,IL1RN,IL1RN-VNTR,1/1
-1203,IL-1 beta,C-511T,C/C
-1203,IL-1 beta,T-31C,T/T
-1203,IL-1 beta,C3953T,C/T
-1203,IL1RN,IL1RN-VNTR,1/2
-1106,IL-1 beta,C-511T,C/T
-1106,IL-1 beta,T-31C,T/C
-1106,IL-1 beta,C3953T,C/C
-1106,IL1RN,IL1RN-VNTR,1/1
-1098,IL-1 beta,C-511T,T/T
-1098,IL-1 beta,T-31C,C/C
-1098,IL-1 beta,C3953T,C/C
-1098,IL1RN,IL1RN-VNTR,1/1
-1090,IL-1 beta,C-511T,C/C
-1090,IL-1 beta,T-31C,T/T
-1090,IL-1 beta,C3953T,C/C
-1090,IL1RN,IL1RN-VNTR,1/1
-1112,IL-1 beta,C-511T,C/T
-1112,IL-1 beta,T-31C,T/C
-1112,IL-1 beta,C3953T,C/C
-1112,IL1RN,IL1RN-VNTR,1/2
-1212,IL-1 beta,C-511T,C/T
-1212,IL-1 beta,T-31C,T/C
-1212,IL-1 beta,C3953T,C/T
-1213,IL-1 beta,C-511T,C/T
-1213,IL-1 beta,T-31C,T/C
-1213,IL-1 beta,C3953T,C/C
-1137,IL-1 beta,C-511T,C/C
-1137,IL-1 beta,T-31C,T/T
-1137,IL-1 beta,C3953T,C/T
-1137,IL1RN,IL1RN-VNTR,1/1
-1136,IL-1 beta,C-511T,C/C
-1136,IL-1 beta,T-31C,T/T
-1136,IL-1 beta,C3953T,C/T
-1136,IL1RN,IL1RN-VNTR,2/2
-1128,IL-1 beta,C-511T,T/T
-1128,IL-1 beta,T-31C,C/C
-1128,IL-1 beta,C3953T,C/C
-1128,IL1RN,IL1RN-VNTR,1/1
-1120,IL-1 beta,C-511T,C/C
-1120,IL-1 beta,T-31C,T/T
-1120,IL-1 beta,C3953T,C/T
-1120,IL1RN,IL1RN-VNTR,1/1
-1104,IL-1 beta,C-511T,C/C
-1104,IL-1 beta,T-31C,T/T
-1104,IL-1 beta,C3953T,C/C
-1104,IL1RN,IL1RN-VNTR,2/2
-1144,IL-1 beta,C-511T,C/T
-1144,IL-1 beta,T-31C,T/C
-1144,IL-1 beta,C3953T,C/C
-1144,IL1RN,IL1RN-VNTR,1/2
-1089,IL-1 beta,C-511T,C/T
-1089,IL-1 beta,T-31C,T/C
-1089,IL-1 beta,C3953T,C/C
-1089,IL1RN,IL1RN-VNTR,1/1
-1097,IL-1 beta,C-511T,C/T
-1097,IL-1 beta,T-31C,T/C
-1097,IL-1 beta,C3953T,C/C
-1097,IL1RN,IL1RN-VNTR,1/2
-1105,IL-1 beta,C-511T,C/T
-1105,IL-1 beta,T-31C,T/C
-1105,IL-1 beta,C3953T,C/C
-1105,IL1RN,IL1RN-VNTR,1/2
-1113,IL-1 beta,C-511T,T/T
-1113,IL-1 beta,T-31C,C/C
-1113,IL-1 beta,C3953T,C/T
-1113,IL1RN,IL1RN-VNTR,1/1
-1121,IL-1 beta,C-511T,C/C
-1121,IL-1 beta,T-31C,T/T
-1121,IL-1 beta,C3953T,C/C
-1121,IL1RN,IL1RN-VNTR,1/1
-1129,IL-1 beta,C-511T,C/C
-1129,IL-1 beta,T-31C,T/T
-1129,IL-1 beta,C3953T,C/T
-1129,IL1RN,IL1RN-VNTR,1/1
-1214,IL-1 beta,C-511T,C/T
-1174,IL1RN,IL1RN-VNTR,1/1
-1210,IL-1 beta,T-31C,T/T
-1210,IL-1 beta,C3953T,C/C
-1162,IL-1 beta,C-511T,C/T
-1162,IL-1 beta,T-31C,T/C
-1162,IL-1 beta,C3953T,C/C
-1162,IL1RN,IL1RN-VNTR,1/2
-1163,IL-1 beta,C-511T,C/T
-1163,IL-1 beta,T-31C,T/C
-1163,IL-1 beta,C3953T,C/C
-1163,IL1RN,IL1RN-VNTR,1/1
-1164,IL-1 beta,C-511T,C/T
-1164,IL-1 beta,T-31C,T/C
-1164,IL-1 beta,C3953T,C/C
-1164,IL1RN,IL1RN-VNTR,2/2
-1149,IL-1 beta,C-511T,C/C
-1149,IL-1 beta,T-31C,T/T
-1149,IL-1 beta,C3953T,C/C
-1149,IL1RN,IL1RN-VNTR,2/4
-1150,IL-1 beta,C-511T,C/T
-1150,IL-1 beta,T-31C,T/C
-1150,IL-1 beta,C3953T,C/C
-1151,IL-1 beta,C-511T,T/T
-1151,IL-1 beta,T-31C,C/C
-1151,IL-1 beta,C3953T,C/C
-1151,IL1RN,IL1RN-VNTR,1/2
-1211,IL-1 beta,C-511T,T/T
-1211,IL-1 beta,T-31C,C/C
-1211,IL-1 beta,C3953T,C/C
-1107,IL-1 beta,C-511T,C/C
-1107,IL-1 beta,T-31C,T/T
-1107,IL-1 beta,C3953T,C/C
-1107,IL1RN,IL1RN-VNTR,1/2
-1115,IL-1 beta,C-511T,C/T
-1115,IL-1 beta,T-31C,T/C
-1115,IL-1 beta,C3953T,C/T
-1115,IL1RN,IL1RN-VNTR,1/2
-1123,IL-1 beta,C-511T,T/T
-1123,IL-1 beta,T-31C,C/C
-1123,IL-1 beta,C3953T,C/C
-1123,IL1RN,IL1RN-VNTR,1/1
-1131,IL-1 beta,C-511T,C/T
-1131,IL-1 beta,T-31C,T/C
-1131,IL-1 beta,C3953T,C/C
-1131,IL1RN,IL1RN-VNTR,1/1
-1139,IL-1 beta,C-511T,C/C
-1139,IL-1 beta,T-31C,T/T
-1139,IL-1 beta,C3953T,C/C
-1139,IL1RN,IL1RN-VNTR,1/2
-1147,IL-1 beta,C-511T,C/T
-1147,IL-1 beta,T-31C,T/C
-1147,IL-1 beta,C3953T,C/T
-1147,IL1RN,IL1RN-VNTR,1/2
-1204,IL-1 beta,C-511T,C/T
-1204,IL-1 beta,T-31C,T/C
-1204,IL-1 beta,C3953T,C/T
-1204,IL1RN,IL1RN-VNTR,1/2
-1189,IL-1 beta,C-511T,C/T
-1189,IL-1 beta,T-31C,T/C
-1189,IL-1 beta,C3953T,C/C
-1189,IL1RN,IL1RN-VNTR,1/1
-1190,IL-1 beta,C-511T,C/T
-1190,IL-1 beta,T-31C,T/C
-1190,IL-1 beta,C3953T,C/T
-1190,IL1RN,IL1RN-VNTR,1/1
-1191,IL-1 beta,C-511T,T/T
-1191,IL-1 beta,T-31C,C/C
-1191,IL-1 beta,C3953T,C/C
-1191,IL1RN,IL1RN-VNTR,1/2
-1192,IL-1 beta,C-511T,C/T
-1192,IL-1 beta,T-31C,T/C
-1192,IL-1 beta,C3953T,C/T
-1192,IL1RN,IL1RN-VNTR,1/1
-1193,IL-1 beta,C-511T,C/T
-1193,IL-1 beta,T-31C,T/C
-1193,IL-1 beta,C3953T,C/C
-1193,IL1RN,IL1RN-VNTR,1/1
-1194,IL-1 beta,C-511T,C/C
-1194,IL-1 beta,T-31C,T/T
-1194,IL-1 beta,C3953T,T/T
-1194,IL1RN,IL1RN-VNTR,1/2
-1195,IL-1 beta,C-511T,C/T
-1195,IL-1 beta,T-31C,T/C
-1195,IL-1 beta,C3953T,C/T
-1195,IL1RN,IL1RN-VNTR,1/1
-1196,IL-1 beta,C-511T,T/T
-1196,IL-1 beta,T-31C,C/C
-1196,IL-1 beta,C3953T,C/C
-1196,IL1RN,IL1RN-VNTR,1/2
-1181,IL-1 beta,C-511T,C/C
-1181,IL-1 beta,T-31C,T/T
-1181,IL-1 beta,C3953T,C/C
-1181,IL1RN,IL1RN-VNTR,2/2
-1182,IL-1 beta,C-511T,C/T
-1182,IL-1 beta,T-31C,T/C
-1182,IL-1 beta,C3953T,C/T
-1182,IL1RN,IL1RN-VNTR,1/2
-1183,IL-1 beta,C-511T,C/T
-1183,IL-1 beta,T-31C,T/C
-1183,IL-1 beta,C3953T,C/T
-1183,IL1RN,IL1RN-VNTR,1/1
-1184,IL-1 beta,C-511T,T/T
-1184,IL-1 beta,T-31C,C/C
-1184,IL-1 beta,C3953T,C/C
-1184,IL1RN,IL1RN-VNTR,1/1
-1185,IL-1 beta,C-511T,C/C
-1185,IL-1 beta,T-31C,T/T
-1185,IL-1 beta,C3953T,C/C
-1185,IL1RN,IL1RN-VNTR,2/3
-1186,IL-1 beta,C-511T,C/C
-1186,IL-1 beta,T-31C,T/T
-1186,IL-1 beta,C3953T,T/T
-1186,IL1RN,IL1RN-VNTR,1/2
-1187,IL-1 beta,C-511T,C/C
-1187,IL-1 beta,T-31C,T/T
-1187,IL-1 beta,C3953T,T/T
-1187,IL1RN,IL1RN-VNTR,1/1
-1188,IL-1 beta,C-511T,C/C
-1188,IL-1 beta,T-31C,T/T
-1188,IL-1 beta,C3953T,C/T
-1188,IL1RN,IL1RN-VNTR,1/2
-1173,IL-1 beta,C-511T,C/T
-1173,IL-1 beta,T-31C,T/C
-1173,IL-1 beta,C3953T,T/T
-1173,IL1RN,IL1RN-VNTR,1/1
-1174,IL-1 beta,C-511T,C/T
-1174,IL-1 beta,T-31C,T/C
-1174,IL-1 beta,C3953T,C/T
-1210,IL-1 beta,C-511T,C/C
-1114,IL-1 beta,T-31C,T/C
-1114,IL-1 beta,C3953T,C/T
-1114,IL1RN,IL1RN-VNTR,1/2
-1122,IL-1 beta,C-511T,C/C
-1122,IL-1 beta,T-31C,T/T
-1122,IL-1 beta,C3953T,C/T
-1122,IL1RN,IL1RN-VNTR,1/1
-1205,IL-1 beta,C-511T,C/T
-1205,IL-1 beta,T-31C,T/C
-1205,IL-1 beta,C3953T,C/C
-1205,IL1RN,IL1RN-VNTR,2/2
-1206,IL-1 beta,C-511T,C/C
-1206,IL-1 beta,T-31C,T/T
-1206,IL-1 beta,C3953T,C/C
-1206,IL1RN,IL1RN-VNTR,2/2
-1207,IL-1 beta,C-511T,C/T
-1207,IL-1 beta,T-31C,T/C
-1207,IL-1 beta,C3953T,C/C
-1207,IL1RN,IL1RN-VNTR,1/2
-1208,IL-1 beta,C-511T,C/C
-1208,IL-1 beta,T-31C,T/T
-1208,IL-1 beta,C3953T,C/T
-1208,IL1RN,IL1RN-VNTR,1/1
-1209,IL-1 beta,C-511T,T/T
-1209,IL-1 beta,T-31C,C/C
-1209,IL-1 beta,C3953T,C/C
-1209,IL1RN,IL1RN-VNTR,2/2
-1197,IL-1 beta,C-511T,C/T
-1197,IL-1 beta,T-31C,T/C
-1197,IL-1 beta,C3953T,C/T
-1197,IL1RN,IL1RN-VNTR,1/2
-1130,IL-1 beta,C-511T,T/T
-1130,IL-1 beta,T-31C,C/C
-1130,IL-1 beta,C3953T,C/C
-1130,IL1RN,IL1RN-VNTR,2/2
-1138,IL-1 beta,C-511T,C/C
-1114,IL-1 beta,C-511T,C/T
-1138,IL-1 beta,T-31C,T/T
-1138,IL-1 beta,C3953T,C/C
-1138,IL1RN,IL1RN-VNTR,1/1
-1146,IL-1 beta,C-511T,C/T
-1146,IL-1 beta,T-31C,T/C
-1146,IL-1 beta,C3953T,C/C
-1146,IL1RN,IL1RN-VNTR,1/2
-1145,IL-1 beta,C-511T,C/T
-1145,IL-1 beta,T-31C,T/C
-1145,IL-1 beta,C3953T,C/C
-1145,IL1RN,IL1RN-VNTR,1/2
-1091,IL-1 beta,C-511T,C/T
-1091,IL-1 beta,T-31C,T/C
-1091,IL-1 beta,C3953T,C/C
-1091,IL1RN,IL1RN-VNTR,1/2
-1099,IL-1 beta,C-511T,C/T
-1099,IL-1 beta,T-31C,T/C
-1099,IL-1 beta,C3953T,C/T
-1099,IL1RN,IL1RN-VNTR,1/1
-1085,IL-1 beta,C-511T,C/T
-1085,IL-1 beta,T-31C,T/C
-1085,IL-1 beta,C3953T,C/C
-1085,IL1RN,IL1RN-VNTR,1/2
-1093,IL-1 beta,C-511T,C/T
-1093,IL-1 beta,T-31C,T/C
-1093,IL-1 beta,C3953T,C/T
-1093,IL1RN,IL1RN-VNTR,1/1
-1101,IL-1 beta,C-511T,T/T
-1101,IL-1 beta,T-31C,C/C
-1101,IL-1 beta,C3953T,C/C
-1101,IL1RN,IL1RN-VNTR,1/2
-1109,IL-1 beta,C-511T,C/T
-1109,IL-1 beta,T-31C,T/C
-1109,IL-1 beta,C3953T,C/C
-1109,IL1RN,IL1RN-VNTR,1/3
-1117,IL-1 beta,C-511T,C/C
-1117,IL-1 beta,T-31C,T/T
-1117,IL-1 beta,C3953T,C/C
-1117,IL1RN,IL1RN-VNTR,1/2
-1125,IL-1 beta,C-511T,C/T
-1125,IL-1 beta,T-31C,T/C
-1125,IL-1 beta,C3953T,C/T
-1125,IL1RN,IL1RN-VNTR,1/2
-1133,IL-1 beta,C-511T,C/T
-1133,IL-1 beta,T-31C,T/C
-1133,IL-1 beta,C3953T,C/C
-1133,IL1RN,IL1RN-VNTR,1/2
-1141,IL-1 beta,C-511T,C/C
-1141,IL-1 beta,T-31C,T/T
-1141,IL-1 beta,C3953T,C/C
-1141,IL1RN,IL1RN-VNTR,1/1
-1086,IL-1 beta,C-511T,T/T
-1086,IL-1 beta,T-31C,C/C
-1086,IL-1 beta,C3953T,C/C
-1086,IL1RN,IL1RN-VNTR,1/2
-1094,IL-1 beta,C-511T,C/C
-1094,IL-1 beta,T-31C,T/T
-1094,IL-1 beta,C3953T,C/T
-1094,IL1RN,IL1RN-VNTR,1/2
-1102,IL-1 beta,C-511T,C/T
-1102,IL-1 beta,T-31C,T/C
-1102,IL-1 beta,C3953T,C/C
-1102,IL1RN,IL1RN-VNTR,1/1
-1110,IL-1 beta,C-511T,C/C
-1110,IL-1 beta,T-31C,T/T
-1110,IL-1 beta,C3953T,C/T
-1110,IL1RN,IL1RN-VNTR,1/1
-1118,IL-1 beta,C-511T,C/T
-1118,IL-1 beta,T-31C,T/C
-1118,IL-1 beta,C3953T,C/C
-1118,IL1RN,IL1RN-VNTR,1/1
-1126,IL-1 beta,C-511T,C/T
-1126,IL-1 beta,T-31C,T/C
-1126,IL-1 beta,C3953T,T/T
-1126,IL1RN,IL1RN-VNTR,1/1
-1134,IL-1 beta,C-511T,C/C
-1134,IL-1 beta,T-31C,T/T
-1134,IL-1 beta,C3953T,C/T
-1134,IL1RN,IL1RN-VNTR,1/1
-1142,IL-1 beta,C-511T,C/T
-1142,IL-1 beta,T-31C,T/C
-1142,IL-1 beta,C3953T,C/C
-1142,IL1RN,IL1RN-VNTR,1/2
-1087,IL-1 beta,C-511T,C/T
-1087,IL-1 beta,T-31C,T/C
-1087,IL-1 beta,C3953T,C/C
-1087,IL1RN,IL1RN-VNTR,1/1
-1095,IL-1 beta,C-511T,C/T
-1095,IL-1 beta,T-31C,T/C
-1095,IL-1 beta,C3953T,C/C
-1095,IL1RN,IL1RN-VNTR,1/3
-1103,IL-1 beta,C-511T,C/T
-1103,IL-1 beta,T-31C,T/C
-1103,IL-1 beta,C3953T,C/C
-1103,IL1RN,IL1RN-VNTR,1/1
-1111,IL-1 beta,C-511T,C/C
-1111,IL-1 beta,T-31C,T/T
-1111,IL-1 beta,C3953T,C/C
-1111,IL1RN,IL1RN-VNTR,1/1
-1119,IL-1 beta,C-511T,T/T
-1119,IL-1 beta,T-31C,C/C
-1119,IL-1 beta,C3953T,C/C
-1119,IL1RN,IL1RN-VNTR,1/1
-1127,IL-1 beta,C-511T,C/C
-1127,IL-1 beta,T-31C,T/T
-1127,IL-1 beta,C3953T,C/T
-1127,IL1RN,IL1RN-VNTR,1/1
-1135,IL-1 beta,C-511T,C/C
-1135,IL-1 beta,T-31C,T/T
-1135,IL-1 beta,C3953T,C/T
-1135,IL1RN,IL1RN-VNTR,1/1
-1143,IL-1 beta,C-511T,C/C
-1143,IL-1 beta,T-31C,T/T
-1143,IL-1 beta,C3953T,C/C
-1143,IL1RN,IL1RN-VNTR,1/1
-1088,IL-1 beta,C-511T,C/C
-1088,IL-1 beta,T-31C,T/T
-1088,IL-1 beta,C3953T,C/T
-1088,IL1RN,IL1RN-VNTR,1/1
-1096,IL-1 beta,C-511T,C/C
-1096,IL-1 beta,T-31C,T/T
-1096,IL-1 beta,C3953T,C/C
-1096,IL1RN,IL1RN-VNTR,1/1
-1100,IL-1 beta,C-511T,T/T
-1100,IL-1 beta,T-31C,C/C
-1100,IL-1 beta,C3953T,C/C
-1100,IL1RN,IL1RN-VNTR,1/2
-1132,IL-1 beta,C-511T,C/T
-1132,IL-1 beta,T-31C,T/C
-1132,IL-1 beta,C3953T,C/T
-1132,IL1RN,IL1RN-VNTR,1/1
-1140,IL-1 beta,C-511T,C/C
-1140,IL-1 beta,T-31C,T/T
-1140,IL-1 beta,C3953T,C/C
-1140,IL1RN,IL1RN-VNTR,1/1
-1148,IL-1 beta,C-511T,C/C
-1148,IL-1 beta,T-31C,T/T
-1148,IL-1 beta,C3953T,C/T
-1148,IL1RN,IL1RN-VNTR,1/2
-1108,IL-1 beta,C-511T,C/C
-1108,IL-1 beta,T-31C,T/T
-1108,IL-1 beta,C3953T,C/C
-1108,IL1RN,IL1RN-VNTR,1/1
-1116,IL-1 beta,C-511T,C/T
-1116,IL-1 beta,T-31C,T/C
-1116,IL-1 beta,C3953T,C/C
-1116,IL1RN,IL1RN-VNTR,1/2
-1124,IL-1 beta,C-511T,C/T
-1124,IL-1 beta,T-31C,T/C
-1124,IL-1 beta,C3953T,C/T
-1124,IL1RN,IL1RN-VNTR,1/1
-1166,IL-1 beta,C-511T,C/T
-1166,IL-1 beta,T-31C,T/C
-1166,IL-1 beta,C3953T,C/C
-1166,IL1RN,IL1RN-VNTR,1/2
-1167,IL-1 beta,C-511T,C/C
-1167,IL-1 beta,T-31C,T/T
-1167,IL-1 beta,C3953T,C/C
-1167,IL1RN,IL1RN-VNTR,1/2
-1168,IL-1 beta,C-511T,C/C
-1168,IL-1 beta,T-31C,T/T
-1168,IL-1 beta,C3953T,T/T
-1168,IL1RN,IL1RN-VNTR,1/1
-1169,IL-1 beta,C-511T,C/C
-1169,IL-1 beta,T-31C,T/T
-1169,IL-1 beta,C3953T,C/C
-1169,IL1RN,IL1RN-VNTR,2/2
-1170,IL-1 beta,C-511T,C/T
-1170,IL-1 beta,T-31C,C/C
-1170,IL-1 beta,C3953T,C/C
-1170,IL1RN,IL1RN-VNTR,1/1
-1171,IL-1 beta,C-511T,C/T
-1171,IL-1 beta,T-31C,T/T
-1171,IL-1 beta,C3953T,C/T
-1171,IL1RN,IL1RN-VNTR,1/2
-1172,IL-1 beta,C-511T,T/T
-1172,IL-1 beta,T-31C,C/C
-1172,IL-1 beta,C3953T,C/C
-1172,IL1RN,IL1RN-VNTR,1/1
-1152,IL-1 beta,C-511T,C/C
-1152,IL-1 beta,T-31C,T/T
-1152,IL-1 beta,C3953T,C/C
-1152,IL1RN,IL1RN-VNTR,1/1
-1153,IL-1 beta,C-511T,C/C
-1153,IL-1 beta,T-31C,T/T
-1153,IL-1 beta,C3953T,C/T
-1153,IL1RN,IL1RN-VNTR,1/2
-1154,IL-1 beta,C-511T,C/T
-1154,IL-1 beta,T-31C,T/C
-1154,IL-1 beta,C3953T,C/T
-1154,IL1RN,IL1RN-VNTR,1/1
-1155,IL-1 beta,C-511T,C/T
-1155,IL-1 beta,T-31C,T/C
-1155,IL-1 beta,C3953T,T/T
-1155,IL1RN,IL1RN-VNTR,1/2
-1156,IL-1 beta,C-511T,C/T
-1156,IL-1 beta,T-31C,T/C
-1156,IL-1 beta,C3953T,C/C
-1156,IL1RN,IL1RN-VNTR,1/3
-1157,IL-1 beta,C-511T,C/T
-1157,IL-1 beta,T-31C,T/C
-1157,IL-1 beta,C3953T,C/C
-1157,IL1RN,IL1RN-VNTR,1/2
-1158,IL-1 beta,C-511T,C/T
-1158,IL-1 beta,T-31C,T/C
-1158,IL-1 beta,C3953T,C/C
-1158,IL1RN,IL1RN-VNTR,1/2
-1159,IL-1 beta,C-511T,C/C
-1159,IL-1 beta,T-31C,T/T
-1159,IL-1 beta,C3953T,C/C
-1159,IL1RN,IL1RN-VNTR,1/2
-1160,IL-1 beta,C-511T,C/T
-1160,IL-1 beta,T-31C,T/C
-1160,IL-1 beta,C3953T,C/C
-1160,IL1RN,IL1RN-VNTR,1/2
-1161,IL-1 beta,C-511T,C/T
-1161,IL-1 beta,T-31C,T/C
-1161,IL-1 beta,C3953T,C/C
-1161,IL1RN,IL1RN-VNTR,1/2
diff -Nru r-cran-genetics-1.3.8/examples/test.data.txt r-cran-genetics-1.3.8.1/examples/test.data.txt
--- r-cran-genetics-1.3.8/examples/test.data.txt	2006-06-29 18:14:28.000000000 +0000
+++ r-cran-genetics-1.3.8.1/examples/test.data.txt	1970-01-01 00:00:00.000000000 +0000
@@ -1,100 +0,0 @@
-Patient ID,Locus,Marker,Genotype
-1028022,P53,C1556G,G/G
-1028022,P53,T127A,A/T
-1028022,P53,T5094A,A/T
-1035130,P53,C1556G,G/G
-1035130,P53,T127A,A/T
-1035130,P53,T5094A,A/T
-1090730,P53,C1556G,G/G
-1090730,P53,T127A,A/A
-1090730,P53,T5094A,A/A
-1266053,P53,C1556G,G/C
-1266053,P53,T127A,A/T
-1266053,P53,T5094A,A/A
-1313129,P53,C1556G,G/C
-1313129,P53,T127A,A/A
-1313129,P53,T5094A,A/A
-1317274,P53,C1556G,G/G
-1317274,P53,T127A,A/T
-1317274,P53,T5094A,A/A
-1490037,P53,C1556G,G/G
-1490037,P53,T127A,A/T
-1490037,P53,T5094A,A/A
-1490938,P53,C1556G,G/G
-1490938,P53,T127A,A/T
-1490938,P53,T5094A,A/A
-1554594,P53,C1556G,G/G
-1554594,P53,T127A,A/A
-1554594,P53,T5094A,A/A
-1588019,P53,C1556G,G/G
-1588019,P53,T127A,A/A
-1588019,P53,T5094A,A/T
-1659908,P53,C1556G,G/G
-1659908,P53,T127A,T/T
-1659908,P53,T5094A,A/T
-1726741,P53,C1556G,G/G
-1726741,P53,T127A,A/A
-1726741,P53,T5094A,A/A
-1963357,P53,C1556G,G/G
-1963357,P53,T127A,A/T
-1963357,P53,T5094A,A/T
-1973699,P53,C1556G,G/G
-1973699,P53,T127A,T/T
-1973699,P53,T5094A,A/A
-2089460,P53,C1556G,G/C
-2089460,P53,T127A,A/A
-2089460,P53,T5094A,A/A
-2100343,P53,C1556G,G/C
-2100343,P53,T127A,A/A
-2100343,P53,T5094A,A/A
-2262462,P53,C1556G,G/G
-2262462,P53,T127A,A/T
-2262462,P53,T5094A,A/A
-2525870,P53,C1556G,G/G
-2525870,P53,T127A,A/A
-2525870,P53,T5094A,A/T
-2655839,P53,C1556G,G/G
-2655839,P53,T127A,T/T
-2655839,P53,T5094A,A/A
-2878777,P53,C1556G,G/G
-2878777,P53,T127A,A/A
-2878777,P53,T5094A,A/A
-2881107,P53,C1556G,G/G
-2881107,P53,T127A,A/A
-2881107,P53,T5094A,A/T
- 288933,P53,C1556G,G/G
- 288933,P53,T127A,A/T
- 288933,P53,T5094A,A/A
-3022102,P53,C1556G,G/G
-3022102,P53,T127A,A/T
-3022102,P53,T5094A,A/T
-3058775,P53,C1556G,G/G
-3058775,P53,T127A,A/A
-3058775,P53,T5094A,A/A
- 313580,P53,C1556G,G/C
- 313580,P53,T127A,T/T
- 313580,P53,T5094A,A/A
-3282544,P53,C1556G,G/G
-3282544,P53,T127A,A/A
-3282544,P53,T5094A,A/A
-3335501,P53,C1556G,G/G
-3335501,P53,T127A,A/A
-3335501,P53,T5094A,A/A
-3345731,P53,C1556G,G/G
-3345731,P53,T127A,A/A
-3345731,P53,T5094A,A/T
-3506399,P53,C1556G,G/G
-3506399,P53,T127A,A/T
-3506399,P53,T5094A,A/A
-3509677,P53,C1556G,G/C
-3509677,P53,T127A,A/A
-3509677,P53,T5094A,A/A
-3521979,P53,C1556G,G/G
-3521979,P53,T127A,A/T
-3521979,P53,T5094A,A/A
-3525409,P53,C1556G,G/G
-3525409,P53,T127A,A/A
-3525409,P53,T5094A,A/A
-3528815,P53,C1556G,G/G
-3528815,P53,T127A,A/A
-3528815,P53,T5094A,A/T
diff -Nru r-cran-genetics-1.3.8/MD5 r-cran-genetics-1.3.8.1/MD5
--- r-cran-genetics-1.3.8/MD5	2012-12-15 06:32:16.000000000 +0000
+++ r-cran-genetics-1.3.8.1/MD5	2013-09-03 10:06:28.000000000 +0000
@@ -1,6 +1,6 @@
 d6a90894caea71aa592b31f61fc60e58 *ChangeLog
-91a46fd915332b12a22f50c6b34c2d55 *DESCRIPTION
-18179ce6f9301cd84deef2d68817d5dc *NAMESPACE
+0152193665622e6323febd48e19b9529 *DESCRIPTION
+a44b4c9703dabb76eb3d4e7ac9da6902 *NAMESPACE
 b8b7201db74480b0deafc4967ea11829 *NEWS
 329130f615d480aa08a6bd96e3755182 *R/HWE.chisq.R
 4d3a1c564741fe0f8adcc7b196ab5e36 *R/HWE.exact.R
@@ -10,13 +10,13 @@
 19b7b0c389f305ef5ef8141ff86e5b75 *R/ci.balance.R
 88958b5bdf8047877f52bb2eb04005dd *R/diseq.R
 7d38f678945174e5b6314e6b875d51b0 *R/expectedGenotypes.R
-0d0c1837ed4d492060a8e0cdf470de95 *R/genotype.R
+c1a6b0430487aec14da9be59e929a94f *R/genotype.R
 6c5b3a399c99aaa56c3e7e74642b06a9 *R/gregorius.R
-fe049f5f71052c044011189b09a6e070 *R/groupGenotype.R
+3f41adad6e782099246e3f701e3d2f75 *R/groupGenotype.R
 528ec9d24b28bd841ad5e9962a971d9f *R/hapmcmc.R
 e3b01c6105b6ea69239e46dd31774354 *R/locus.R
 6fbbbf1406ba97a880435f2a40ed29b7 *R/makeGenotypes.R
-7f90308cf01854f51b6305704a238333 *R/order.genotype.R
+4fd82cb1f0a79962bc6d2469e0c23401 *R/order.genotype.R
 2838edb74732efde60f82e8bd70aa24a *R/plot.LD.R
 b961295af99db991ac477637d013471e *R/plot.genotype.R
 fcfd77197879ac5a267a04d1f33b51a8 *R/power.casectl.R
@@ -25,21 +25,9 @@
 55536419da6dfab22473a8b35cb1e408 *R/summary.genotype.R
 dd6312ac2351213a4377c1a2a1e1c748 *R/write.pedigree.file.R
 d86dd6b301b36ae8906846c9e24652c3 *R/write.pop.file.R
-c4323d94c00f35463a52f53648b48b48 *R/zzz.R
+af5a86eb636340e1c509fc1e0c7a0be2 *R/zzz.R
 f5201d8db362fcd733faf7ed38ca84a8 *TODO
 c056ba3e65d9ad68549fa69904d9c289 *data/gregorius.rda
-b97445c94b50ebd432dba458bf490e99 *examples/Allele_Freq.R
-83d00def581d1954b83003ea514f8404 *examples/Allele_Freq.out
-2e58ef3d59ff9720d224b4dc074db65f *examples/Examples.new
-2e58ef3d59ff9720d224b4dc074db65f *examples/Examples.out
-041b2e0305129d2c247cb58b846bd563 *examples/Gene.examples
-26a6b85e55bae0e84f6b1070769f1314 *examples/Genomics.examples
-1cf27d0172e89cadfd44dcd470d0a40a *examples/HWE_Test.R
-87fa5923d30aea6ca11ca4eb6164bd69 *examples/HWE_Test.out
-67d5f9a4fb11c4c5acd5d4717a9386c1 *examples/locus.example.R
-0eea6c41d38de6d74e5627bae8131e3b *examples/test.ci.R
-06410d63d43f1e0c7a44f8d5cf627e31 *examples/test.data.2.txt
-fe572c37864c85170a9d10aa74c6542a *examples/test.data.txt
 d6a90894caea71aa592b31f61fc60e58 *inst/ChangeLog
 b8b7201db74480b0deafc4967ea11829 *inst/NEWS
 28520aba1e5fa9e753a57cb7655ebd9e *inst/doc/LD.pdf
diff -Nru r-cran-genetics-1.3.8/NAMESPACE r-cran-genetics-1.3.8.1/NAMESPACE
--- r-cran-genetics-1.3.8/NAMESPACE	2011-02-02 02:01:18.000000000 +0000
+++ r-cran-genetics-1.3.8.1/NAMESPACE	2013-09-03 10:02:50.000000000 +0000
@@ -1,3 +1,4 @@
+import(MASS, combinat)
 export(
        HWE.chisq,
        HWE.exact,
diff -Nru r-cran-genetics-1.3.8/R/genotype.R r-cran-genetics-1.3.8.1/R/genotype.R
--- r-cran-genetics-1.3.8/R/genotype.R	2008-04-30 00:54:47.000000000 +0000
+++ r-cran-genetics-1.3.8.1/R/genotype.R	2013-09-03 10:04:08.000000000 +0000
@@ -714,7 +714,7 @@
       ## Extend value first. We do not do this before, since one
       ## might not necessarily like to have B/A together with A/B in
       ## first place.
-      value <- genetics:::.genotype2Haplotype(x=value)
+      value <- .genotype2Haplotype(x=value)
       ## Remove heterozygos matches in goPos
       test <- !(goPos %in% value)
       goPos <- goPos[test]
@@ -727,7 +727,7 @@
       testGOnotAll <- !(goAll %in% value)
       if(any(testGOnotAll)) value <- c(value, goAll[testGOnotAll])
     } else {
-      value <- genetics:::.genotype2Haplotype(x=value)
+      value <- .genotype2Haplotype(x=value)
     }
     attr(x, "genotypeOrder") <- value
   }
@@ -748,14 +748,14 @@
   ## Unique values of x are taken i.e. first occurrence prevails
   ##
   ## Example
-  ## genetics:::.genotype2Haplotype(c("A/A", "A/B", "B/B"))
+  ## .genotype2Haplotype(c("A/A", "A/B", "B/B"))
   ## "A/A" "A/B" "B/A" "B/B"
-  ## genetics:::.genotype2Haplotype(c("B/B", "A/B", "A/A"))
+  ## .genotype2Haplotype(c("B/B", "A/B", "A/A"))
   ## "B/B" "A/B" "B/A" "A/A"
 
   x <- unique(x)
   N <- length(x)
-  parts <- genetics:::.genotype2Allele(x=x)
+  parts <- .genotype2Allele(x=x)
   parts <- rbind(parts, parts[, 2:1])
   ind <- rep(1:N, each=2) + c(0, N)
   parts <- parts[ind, ]
@@ -775,7 +775,7 @@
   ## Coercing to character is done for x.
   ##
   ## Example
-  ## genetics:::.genotype2Allele(c("A/A", "A/B", "B/B"))
+  ## .genotype2Allele(c("A/A", "A/B", "B/B"))
   ##      [,1] [,2]
   ## [1,] "A"  "A"
   ## [2,] "A"  "B"
diff -Nru r-cran-genetics-1.3.8/R/groupGenotype.R r-cran-genetics-1.3.8.1/R/groupGenotype.R
--- r-cran-genetics-1.3.8/R/groupGenotype.R	2007-07-27 17:19:12.000000000 +0000
+++ r-cran-genetics-1.3.8.1/R/groupGenotype.R	2013-09-03 10:04:30.000000000 +0000
@@ -25,7 +25,7 @@
 
   ## Extend the map
   for(i in seq(along=map)) {
-    map[[i]] <- unlist(genetics:::.matchGenotype(alleles=alleles,
+    map[[i]] <- unlist(.matchGenotype(alleles=alleles,
                                                  pattern=map[[i]],
                                                  haplotype=haplotype),
                        use.names=FALSE)
@@ -84,7 +84,7 @@
   ##
   ## Example:
   ## pattern <- c("A/*", "A/B", "*/*", "B/A")
-  ## genetics:::.matchGenotype(alleles=c("B", "A"), pattern=pattern)
+  ## .matchGenotype(alleles=c("B", "A"), pattern=pattern)
   ## $`A/*`
   ## [1] "A/B" "B/A" "A/A"
   ## $`A/B`
@@ -94,7 +94,7 @@
   ## $`B/A`
   ## [1] "B/A" "A/B"
   ##
-  ## genetics:::.matchGenotype(alleles=c("B", "A"), pattern=pattern, haplotype=TRUE)
+  ## .matchGenotype(alleles=c("B", "A"), pattern=pattern, haplotype=TRUE)
   ## $`A/*`
   ## [1] "A/B" "A/A"
   ## $`A/B`
@@ -119,7 +119,7 @@
   names(ret) <- pattern
 
   ## Change * with allele names setup
-  parts <- genetics:::.genotype2Allele(x=pattern)
+  parts <- .genotype2Allele(x=pattern)
   parts <- cbind(parts, 1:nP)
   testStar <- parts == "*"
   nA <- length(alleles)
@@ -140,7 +140,7 @@
         }
       } else {       # */*
         tmp <- expectedHaplotypes(alleles=alleles)
-        tmp <- genetics:::.genotype2Allele(x=tmp)
+        tmp <- .genotype2Allele(x=tmp)
         parts <- rbind(parts, cbind(tmp, i))
       }
     }
@@ -161,7 +161,7 @@
   }
 
   ## For genotype treat A/* the same as */A and A/B as B/A
-  if(!haplotype) ret <- lapply(ret, genetics:::.genotype2Haplotype)
+  if(!haplotype) ret <- lapply(ret, .genotype2Haplotype)
 
   ## Return
   ret
diff -Nru r-cran-genetics-1.3.8/R/order.genotype.R r-cran-genetics-1.3.8.1/R/order.genotype.R
--- r-cran-genetics-1.3.8/R/order.genotype.R	2012-08-14 14:10:00.000000000 +0000
+++ r-cran-genetics-1.3.8.1/R/order.genotype.R	2013-09-03 10:04:37.000000000 +0000
@@ -50,7 +50,7 @@
 
     if(!isHap) {
       ## Match both A/B and B/A
-      genotypeOrder <- genetics:::.genotype2Haplotype(x=genotypeOrder)
+      genotypeOrder <- .genotype2Haplotype(x=genotypeOrder)
     }
     tmp <- match(x, genotypeOrder)
   }
diff -Nru r-cran-genetics-1.3.8/R/zzz.R r-cran-genetics-1.3.8.1/R/zzz.R
--- r-cran-genetics-1.3.8/R/zzz.R	2007-11-20 20:23:10.000000000 +0000
+++ r-cran-genetics-1.3.8.1/R/zzz.R	2013-09-03 10:01:15.000000000 +0000
@@ -1,14 +1,14 @@
 ## $Id: zzz.R 1330 2007-11-20 20:23:12Z warnes $
 
 # Obsoleted by Proper use the DESCRIPTION and NAMESPACE files
-.onLoad <- .First.lib <- function(libname, pkgname)
+.onAttach <- function(libname, pkgname)
 {
-	cat("\n")
-        cat("NOTE: THIS PACKAGE IS NOW OBSOLETE.\n")
-	cat("\n")
-	cat("  The R-Genetics project has developed an set of enhanced genetics\n")
-	cat("  packages to replace 'genetics'. Please visit the project homepage\n")
-        cat("  at http://rgenetics.org for informtion.\n")
-	cat("\n")
+	packageStartupMessage("\n")
+        packageStartupMessage("NOTE: THIS PACKAGE IS NOW OBSOLETE.\n")
+	packageStartupMessage("\n")
+	packageStartupMessage("  The R-Genetics project has developed an set of enhanced genetics\n")
+	packageStartupMessage("  packages to replace 'genetics'. Please visit the project homepage\n")
+        packageStartupMessage("  at http://rgenetics.org for informtion.\n")
+	packageStartupMessage("\n")
 	
 }