v2.1-1
2024-10-25
- Removed warnings and notes after checking the package using R-2.1.0

v2.0-0
2020-08-23
- Added dscore function
- Added related function
- Changed email address after receiving Brian's email

v1.9-2
2014-04-22
- fixed bug in tableHWE function (see e-mail from Martin Rijlaarsdam)

v1.9-1
2013-09-05 (after being removed from CRAN)
- mclapply with parallel
- fixed problems with gfotran (scanWGassociation changes)

v1.9-0
2013-09-05 
- mclapply

v1.8-5
2012-12-17 
- bug fixed: spandSetupSNP function deals properly with 100% missing genotypes

v1.8-4
2012-05-12 
- change: scanWGassociation (.Internal problems see e-mail from B. Ripley)
- change: other Warnings after checking the package using R-1.5.1

v1.8-3
2012-05-09 
- anova.glm labels (see Peter's e-mail) also changed in interactionPval function

v1.8-2
2012-05-03 
- Dropped dependency on goat by adding trim and interleave

v1.8-1
2011-11-22 (Changes to R-2.14.0)
- require has been removed from firstlib function
- HapMap.rda has been resaved using better compression tools::resaveRdaFiles()
- anova.glm does not returns "P(>|Chi|)"[2]  ->  changed to  t1[2, grep("^P.*Chi",names(t1))] (Peter's e-mail)
     - functions changed: intervals.dif, intervals.or, table.interaction, interactionPval

v1.8-0
2011-09-14
- bug fixed: problems when only 1 SNP is analyzed (see Victor's e-mail)
- bug fixed: summary.snp does not compute the HWE when only two genotypes are available (see Victor's e-mail)

v1.7-0
2011-02-28
- bug fixed: problem with heterozygous codes (see Ross Whetten's e-mail)
- added: a new function to compute the exact probability of a genetic score

v1.6-1
2010-09-26
- added: some extra-code to consider G-statistic equal to 0 after Jiexun's comment

v1.6-0
2009-07-17
- changed: labels of plots for p-values (-log[10])

v1.5-9
2009-07-04
- changes in [.WGassociation 
- added: GenomicControl now deals with 2 d.f. chi-square test (e.g., codominant)
- changes in plot.WGassociation 

v1.5-8
2009-03-09
- changed: NAMESPACE includes methods for LD

v1.5-7
2009-03-04
- print.LD file added

v1.5-6
2009-02-06
- Changes in .Rd files to pass 'Rd files against version 2 parser' (R version 2.9.0)

v1.5-5
2008-12-12
- changed: 'association.fit' and 'association' to incorporate the possibility of using other arguments included in 'glm' function such as 'weigths'. Question posted by Ane Marie Closter

-changed: 'plot.WGassociation' to show -log_10(p-values) instead of -log_10(p-values). Question posted by 


v1.5-4
2008-05-29
- changed: 'association.fit' problems with factors and levels to determine when a snp is monomorphic [table(as.character(var)) instead of length(levels(var)) ]


v1.5-3
2008-04-29
- modified: intervals.haplo.glm.R
- added: summary and print for LD objects
- modified: Bonferroni.sig (number of tests when no monomorphic SNPs) 
- added: 'gdata' dependence

v1.5-2
2008-04-22
- added: LD functions adapted from LDplot in package genetics by Gregory Warnes et al.

v1.5-1
2008-03-27
- change in tableHWE to correct deal with strata option
- expandsetupSNP.R has been modified
- summary.snp has been modified and print.summary.snp has been created and added to the NAMESPACE

v1.4-9
2007-10-16
- modified: expandsetupSNP.R to show alleles sorted by frequency when summary of an object of class 'setupSNP' is executed
- changed: e-mail address of the maintainer
- removed: obsolete markup \non_function{}

v1.4-8
2007-05-21
- mvtnorm is required (change in DESCRIPTION, NAMESPACE and firstlib.R)
- added: new generic function maxstat (to compute asymptotic p values for max-statistic) and some methods
- added: function for inspecting overdispersion due to population substructure (qqpval)
- added: function for correcting the p values using genomic control (GenomiControl)
- added: example in the Rd file for odds function
- added: argument nIndiv in association.fit (to deal with genotypeRate properly). association has also been changed (look for 'nSubject')
- minor change in the function snp (when snp is applied to an object of class snp)
- added: reference of SNPassoc to some .Rd files

v1.4-7
2007-05-17
- bug fixed: overdominant returned wrong levels (thanks to Nicholas Orr)

2007-05-02
- bug fixed: [<-.setupSNP  added any variable as new SNP, but could be a covariate
- bug fixed: odds returns NA for monomorphic SNPs
- bug fixed: association.fit detected monomorphic SNPs that were not so

2007-04-02
-bug fixed: c.WGassociation when more than 2 files were combined
-bug fixed: [.WGassociation when rows/columns were selected by name wrong selection was done
-bug fixed: [.WGassociation now also subsets permuted SNPs if available
-changed: [.setupSNP should be faster and preserve snp attributes
-changed: glm2 in table.corner updated to avoid warnings if response was factor
-new function odds to extract odds ratios, 95% CI and p values for a given model from an WGassociation object
-new function [.snp, version of factor that preserves attributes
-new function print.snp


v1.4-6
2007-03-22
- change in 'association' function to deal with SNP with 0% of genotype rate (e.g. all missing) when ajusted models are fitted

v1.4-5
2007-03-20
- bug fixed in the output labels for overdominant model

v1.4-4
2007-03-02
- bug fixed in the function 'intervals.haplo.glm'
- added new functions: codominant.snp, dominant.snp, recessive.snp, overdominant.snp 
- [.WGassociation is able to select using logical statements 
- [.setupSNP recover 'allele.labels' from the SNPs
- perm.Test changed options(warn=-1) to avoid waning messages to fit the beta distribution

v1.4-3
2007-01-22
- removed the file Makevars.win to ../src 
- changed SNPassoc.f to be compiled using g77
- \usage sections for 'SNPassoc-internal' 'plot.WGassociation' and 'snp' have been fixed for S3 methods

v1.4-2
2007-01-19
- added the file Makevars.win to ../src 

v1.4-1
2007-01-17
- minor changes in scanWGassociation
- implemented rank truncated product in permTest function

v1.4
2006-12-12
- minor changes in print.WGassociation 
- zzz.R is replaced by firstlib.R
- firstlib.R calls to a Fortran dll
- created a Fortran program SNPassoc.f which is called from scanWGassociation
- added a new argument to scanWGassociation function called "nperm"
- added a new function called permTest to extract p values from permutation test obtained using scanWGassociation function
- added methods for objects of class "permTest"

v1.3  
2006-11-27
- snp, summary.snp and expandsetupSNP fixed to deal with SNP with 100% missing information

2006-11-26
- manual for WGstats moved to WGassociation
- summary.GWassociation (previous WGstats) fixed

2006-11-25
- interactionPval now accepts only response and asumes formula response~1
- summary.WGassociation and WGstats swapped
- summary.WGassociation generates output even if no info is supplied (whole dataset)

2006-11-23
- added methods for extraction and modification of setupSNP and WGassociation objects 
- genetic model functions generic
- methods: default: recode (accepts snp, numeric, factor or character max 3 values)
		  WGassociation: extracts pvalues for that model




