Changes in version 1.4.2:

    o   Updated GdsReader for compatibility with gdsfmt 0.9.11 (no longer
	compatible with older versions).

Changes in version 1.3.16:

    o   Added convertVcfGds to extract bi-allelic SNPs from a VCF file.

    o   Added ncdfImputedDosage to convert output from common imputation
	programs to NetCDF.  assocTestRegression has an additional argument
	dosage=TRUE to be used with these files.

    o   Added vignette describing GWASTools data structures.

Changes in version 1.3.15:

    o   Bug fix in pedigreePairwiseRelatedness related to use of character
	identifiers.

Changes in version 1.3.14:

    o   assocTestRegression returns NA for snps where cases or controls are
	monomorphic, added assocTestFisherExact to use in that case.

    o   Added snp.exclude argument to pseudoautoIntensityPlot.

    o   Bug fix in messages reporting file read times when creating or
	checking netCDF files.

Changes in version 1.3.13:

    o   Added vignette on converting VCF to NetCDF with annotation.

    o   Prevent duplicateDiscordance from checking correlation by SNP in
	cases of no variation.

Changes in version 1.3.12:

    o   Added GdsReader and GdsGenotypeReader classes with dependency on
	gdsfmt.  GenotypeData objects can also be created with
	GdsGenotypeReader objects in the "data" slot.

Changes in version 1.3.11:

    o   Fixed bug in duplicateDiscordance when Y chromosome is not
	included.

Changes in version 1.3.10:

    o   Fixed bug in chromIntensityPlot so ideogram scales correctly if
	SNPs are excluded.

Changes in version 1.3.9:

    o   Fixed bug in assocTestCPH that could lead to false positives if
	additive model failed but GxE model did not.

    o   Allow multiple variables for stratified analysis in assocTestCPH.

Changes in version 1.3.8:

    o   Pedigree functions accept non-numeric identifiers and provide
	additional output.

Changes in version 1.3.7:

    o   In batchChisqTest, Yates correction cannot be bigger than the terms
	it corrects.  Changed to match bug fix to chisq.test in R 2.15.1.

Changes in version 1.3.6:

    o   Removed automatic subtitle from qqPlot.

    o   Allow selection of theoretical boundaries to draw in ibdPlot.

Changes in version 1.3.5:

    o   Added function asSnpMatrix to convert a GenotypeData object to a
	SnpMatrix object for use with snpStats.

Changes in version 1.3.4:

    o   Added chromosome ideograms to chromIntensityPlot and anomStatsPlot.
	anomStatsPlot has an option to put multiple anomalies on the same
	plot.

Changes in version 1.3.3:

    o   Updated vignette.

Changes in version 1.3.2:

    o   Use lazy loading of data.

    o   manhattanPlot and snpCorrelationPlot accept character vectors of
	chromosome; chrom.labels argument no longer used.

Changes in version 1.3.1:

    o   close method of NcdfReader returns invisibly.

Changes in version 1.1.9:

    o   anomSegStats checks for SNPs in centromere gaps.

    o   anomStatsPlot has option to plot LRR/BAF individually (for greater
	flexibility in layout).

    o   Updates to arguments for plot titles in chromIntensityPlot,
	anomStatsPlot, and pseudoautoIntensityPlot for consistency.

    o   plinkCheck has map.alt argument to override default GenotypeData ->
	PLINK annotation conversion.

Changes in version 1.1.8:

    o   Updated positions of pseudoautosomal regions.

    o   Added plinkToNcdf to convert PLINK files to NetCDF for use in
	GWASTools.

Changes in version 1.1.7:

    o   chromIntensityPlot and pseudoautoIntensityPlot have cex=0.5 by
	default.

    o   chromIntensityPlot colors now match anomStatsPlot colors.

    o   plinkCheck has options to skip checking parents and sex.

    o   plinkCheck sorts alleles by character to avoid phase mismatches.

    o   plinkWrite and plinkCheck print progress messages if verbose=TRUE.

Changes in version 1.1.6:

    o   duplicateDiscordance and duplicateDiscordanceAcrossDatasets use
	only one pair of scans per subject by default.

    o   duplicateDiscordanceProbability sets small negative values to 0.

Changes in version 1.1.5:

    o   duplicateDiscordance has an option to compute correlation by SNP.

    o   Added scan.exclude argument to plinkCheck.

Changes in version 1.1.4:

    o   Added ncdfSetMissingGenotypes function.

    o   plinkCheck now writes a log file with all mismatches found.

    o   duplicateDiscordance excludes Y chrom SNPs for females.

    o   duplicateDiscordance has an option to consider only pairs involving
	the minor allele.

Changes in version 1.1.3:

    o   batchChisqTest and batchFisherTest now return n results for n
	batches even if n=2.

    o   batchFisherTest has return.by.snp=FALSE as default.

Changes in version 1.1.2:

    o   Added LR tests to assocTestRegression.

    o   Bug fix in calculation of mean odds ratio in batchFisherTest.

    o   Bug fix in missingGenotypeByScanChrom for data sets with only one
	female.

Changes in version 1.1.1:

    o   Added functions plinkWrite and plinkCheck for writing and checking
	PLINK ped and map files.

    o   Added pcaSnpFilters data set for identifying regions with high
	PC-SNP correlation.