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.