Changes in version 1.8.1: o Bug fix in getChromosome method for SnpAnnotationDataFrame (proper behavior of unnamed "index" argument). Changes in version 1.7.8: o Added gdsSetMissingGenotypes, updated argument names in ncdfSetMissingGenotypes. o Changed colorscheme in manhattanPlot.R. o Bug fix in ibdPlot - diagonal orange bars are back. o Bug fix in plinkWrite for writing just one sample. o Bug fix in printing pedigreeCheck error message. Changes in version 1.7.7: o Changed handling of GxE interaction variables in assocTestRegression. Changes in version 1.7.6: o Updated vignette for SNPRelate 0.9.16. Changes in version 1.7.5: o gwasExactHW will run on all chromosomes except (Y,M), rather than (autosome,X,XY) only. Changes in version 1.7.4: o More informative error messages in anomDetectBAF and anomDetectLOH. Changes in version 1.7.3: o Changed labeling of IBD plots from "HS" to "Deg2" and "FC" to "Deg3." o Bug fix in pedigreePairwiseRelatedness - no more warning about multiple values passed to stringsAsFactor. o pedigreeClean and pedigreeFindDuplicates are now defunct. Use pedigreeCheck instead. Changes in version 1.5.9: o assocTestRegression computes allele counts separately for each model. o convertNcdfGds uses information from a SnpAnnotationDataFrame to store allele and chromosome codes in the GDS file. Changes in version 1.5.8: o Adding missing value support to GdsReader. o Fixed bug in getAttribute method for GdsReader. o Updated GdsReader for compatibility with gdsfmt 0.9.11 (no longer compatible with older versions). Changes in version 1.5.7: o Fixed bug in genotypeToCharacter that resulted in calls to getGenotype(char=TRUE) for a single SNP to return NA. o Renamed minorAlleleSensitivitySpecificity to minorAlleleDetectionAccuracy and added additional output. Changes in version 1.5.6: o Added function minorAlleleSensitivitySpecificity. Changes in version 1.5.5: o Deprecated pedigreeClean and pedigreeFindDuplicates. pedigreeCheck now encompasses all pedigree checks and should be used instead. o Added pedigreeMaxUnrelated to find the maximum set of unrelated members of a pedigree. o Added additional output column "MAF" to matrix returned by alleleFrequency. Changes in version 1.5.4: o Removed hard-coding of autosomes as 1:22; can now set a vector of integer codes corresponding to autosomes with "autosomeCode" argument at object creation and retrieve with "autosomeCode" methods. This change makes GWASTools compatible with non-human organisms. o Added option to duplicateDiscordanceAcrossDatasets to count missing data as discordance. o Added option to start axes of genoClusterPlot at 0. Changes in version 1.5.3: o Removed "alleleA.col" and "alleleB.col" options from plink functions, as "alleleA" and "alleleB" are now standard names. o Added "getAlleleA" and "getAlleleB" methods to GdsGenotypeReader. o Added "getDimension" method to NcdfReader. Changes in version 1.5.2: o Added "getAlleleA" and "getAlleleB" methods to SnpAnnotation* and GenotypeData objects. o Added genotypeToCharacter function to convert genotypes from number of A alleles to A/B format. o getGenotype for GenotypeData has option char=TRUE to return character genotypes in A/B format. Changes in version 1.5.1: o Added option to duplicateDiscordanceAcrossDatasets to calculate minor allele discordance. 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.