Changes in version 2.9.3: o New methods assocTestSingle and assocTestAggregate are refactors of assocTestMM and assocTestSeq/assocTestSeqWindow, respectively. assocTestSeq and assocTestSeqWindow are deprecated. assocTestMM is still used for GenotypeData objects, but will be deprecated in a future release. fitNullModel is a refactor of fitNullMM/fitNullReg and should be used with the new association test methods. Changes in version 2.7.4: o In fitNullMM, for Binomial and Poisson GLM families, the variance of the fixed effects will not be multiplied by the dispersion parameter RSS. Changes in version 2.7.3: o Change defaults in assocTestSeq*: Davies method for SKAT p-values, flat weights. Changes in version 2.6.0: o Major bug fix: assocTestSeq no longer drops some variants from aggregate tests in the case where the same variants are included in more than one aggregate unit. o Added function for analysis of admixture mapping data. Changes in version 2.2.0: o Added support for sequence data files created with the SeqArray package. o Added functions for Burden and SKAT tests of sequence data. Changes in version 2.0.0: o Added functions for PC-Relate. PC-Relate provides model-free estimation of recent genetic relatedness in general samples. It can be used to estimate kinship coefficients, IBD sharing probabilities, and inbreeding coefficients using genome-wide SNP data. PC-Relate accounts for population structure (ancestry) among sample individuals through the use of ancestry representative principal components (PCs) to provide accurate relatedness estimates due only to recent family (pedigree) structure. o GENESIS now imports the package gdsfmt. Changes in version 1.1.1: o Changed a few default values: MAF filter from 0.05 to 0.01; kin.thresh from 0.025 to 2^(-11/2) ~ 0.022; div.thresh from -0.025 to -2^(-11/2) ~ -0.022; v (the number of PCs returned) from 10 to 20 o Changed the argument 'block.size' to 'snp.block.size' o Slightly altered the command line reporting when verbose = TRUE Changes in version 0.99.4: o Fixed a minor bug to zero out diagonal of divMat in pcairPartition() Changes in version 0.99.0: o Initial version of GENESIS. Contains functionality to perform PC-AiR.