Set extremely small p-values (< Machine$double.xmin) calculated with pchisq to Machine$double.xmin. This change prevents GENESIS from returning p-values equal to 0.
Add new test option "fastSMMAT" to assocTestAggregate.
Fixed a bug in pcrelate when running with both multiple sample blocks and multiple cores
Fixed a bug in assocTestSingle for computing saddle-point approximation (SPA) p-values for variants (i.e. when using test = Score.SPA) when the input null model is not a mixed models (i.e. when fitNullModel was run with cov.mat = NULL , or all variance components converged to 0) and the family = "binomial"
Subset covariance matrix to specified samples when sample.id argument is passed to fitNullModel when called with an AnnotatedDataFrame
Added option for recessive and dominant coding to assocTestSingle.
Implement MatrixGenotypeReader method for pcair by writing a temporary GDS file.
assocTestSingle, assocTestAggregate, admixMap, and pcrelate use the BiocParallel package for parallel execution on blocks of variants.
For assocTestAggregate, the total number of genotypes in a single iterator element (NxM where N=number of samples and M=number of variants) may be >2^31.
Added functions to compute variant-specific inflation factors.
Added the option to perform a fast approximation to the score standard error in assocTestSingle. New function nullModelFastScore prepares a null model to be used with this option.
Updated structure of fitNullModel objects. Null model objects with the previous structure will be automatically updated with a warning, but you may want to consider rerunning 'fitNullModel' if you plan to use an older null model with the current version.
For BionomiRare, always restrict to variants where alt=minor allele.
Change default value of small.samp.correct in pcrelate to TRUE.
Add options to remove NxN matrices from a null model (function nullModelSmall and fitNullModel argument return.small).
Add check for collinearity in covariates.
Add test options "BinomiRare" and "CMP" to assocTestSingle and assocTestAggregate.
Add function jointScoreTest to perform a joint score test of a set of variants using a null model and a matrix of genotype dosages.
Add function effectAllele to return the effect allele for association tests.
Force design matrices to be non-sparse.
Fix a bug that prevented use of multiple environment variables in GxE.
Allow divergence to be NULL in pcair and pcairPartition.
Fix a bug in null model when starting variance component is close to 0.
Add option "Score.SPA" to assocTestSingle. This option for binary outcomes uses the saddlepoint approximation to compute p-values and is recommended for unbalanced case/control ratios.
"Wald" is no longer a test option in assocTestSingle. Instead, the Score test is always run, and "Est" (an estimation of the Wald test beta) is always returned also. The values in the "Est" are identical to what was previously returned by test="Wald".
Since the only single-variant test option is "Score", "burden.test" is no longer an option in assocTestAggregate. Output returned is now identical to that described above for assocTestSingle.
Add option "fastSKAT" to assocTestAggregate. Some other arguments and names of output columns for SKAT tests have also changed. This update includes code from the bigQF package (https://github.com/tslumley/bigQF). With the addition of C code, GENESIS now requires compilation.
Remove all monomorphic variants (including all heterozygotes) from association test results.
Restore option to run pcair without kinship matrix.
Add option to use imputed dosage in association tests.
pcair and pcrelate have been completely rewritten for better consistency with other methods. Some argument names have changed; see the documentation. The output of pcrelate is now a list of data.frames instead of a list of matrices.
pcrelateReadKinship and pcrelateReadInbreed are deprecated, as these tables are now returned by pcrelate.
pcrelateMakeGRM is deprecated; use pcrelateToMatrix with new pcrelate output format.
king2mat is deprecated; use kingToMatrix instead.
fitNullMM, fitNullReg, assocTestMM, and admixMapMM are deprecated. assocTestSeq and assocTestSeqWindow are defunct. Use fitNullModel, assocTestSingle, assocTestAggregate, and admixMap instead.
Refactor pcrelate.
Added assocTestAggregate method for GenotypeData objects.
Refactor pcair.
Added admixMap function to replace admixMapMM.
Added assocTestSingle and fitNullModel methods for GenotypeData objects.
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.
In fitNullMM, for Binomial and Poisson GLM families, the variance of the fixed effects will not be multiplied by the dispersion parameter RSS.
Change defaults in assocTestSeq*: Davies method for SKAT p-values, flat weights.
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.
Added function for analysis of admixture mapping data.
Added support for sequence data files created with the SeqArray package.
Added functions for Burden and SKAT tests of sequence data.
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.
GENESIS now imports the package gdsfmt.
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
Changed the argument 'block.size' to 'snp.block.size'
Slightly altered the command line reporting when verbose = TRUE
Fixed a minor bug to zero out diagonal of divMat in pcairPartition()
Initial version of GENESIS. Contains functionality to perform PC-AiR.