CHANGES IN VERSION 2.4.0 ------------------------- o update `seqFitLDpruning()` o reduce the memory usage in `seqAssocGLMM_SPA()` when the genotype file is not split by chromosomes CHANGES IN VERSION 2.2.1 ------------------------- o fix the compiler warning: -Wformat-security o fix a compiler issue with gcc v7.5 CHANGES IN VERSION 2.2.0 ------------------------- o fix the "Matrix-deprecated" warning from the Matrix package when calling `as(, "dgCMatrix")` CHANGES IN VERSION 2.0.0 ------------------------- NEW FEATURES o New features to use sparse genetic relationship matrix in generalized linear mixed models (GLMMs) according to the SAIGE-GENE paper (Zhou et al., 2020) o a new argument 'grm.mat' in `seqFitNullGLMM_SPA()`: the dense or sparse genetic relationship matrix (GRM) can be specified via 'grm.mat' o MAC categories for multiple variance ratios in `seqFitNullGLMM_SPA()`, `seqAssocGLMM_SPA()`, designed for rare variants o new function `seqAssocGLMM_SKAT()` for the SKAT aggregate method o new feature `seqAssocGLMM_ACAT_O()` to include the SKAT aggregate method for full ACAT-O tests o faster `seqSAIGE_LoadPval()` when merging multiple input files CHANGES IN VERSION 1.12.4 ------------------------- o fix the compiling issue on ARM64 (see https://github.com/AbbVie-ComputationalGenomics/SAIGEgds/issues/8) CHANGES IN VERSION 1.12.1 ------------------------- o fix the memory issue because of using deprecated tbb::task_scheduler_init in RcppParallel CHANGES IN VERSION 1.6.0 ------------------------- o `seqFitNullGLMM_SPA()` can use imputed dosages directly without converting the dosages to the best-guess genotypes o new function `glmmHeritability()` for approximate heritability estimates CHANGES IN VERSION 1.4.0 ------------------------- o set-based tests: burden, ACAT-V CHANGES IN VERSION 1.2.2 ------------------------- o update the citation o work around gcc-10 CHANGES IN VERSION 1.2.0 ------------------------- o `seqAssocGLMM_SPA()` can save to a RDS file CHANGES IN VERSION 1.0.2 ------------------------- o fix an issue when there is no covariate in the formula (e.g., y ~ 1) CHANGES IN VERSION 1.0.1 ------------------------- o add a new option for the threshold of missing variant to `seqAssocGLMM_SPA()` o change the output column 'AC.alt' to 'mac' in `seqAssocGLMM_SPA()` o retry model fitting at least 10 times if matrix is singular or not positive definite, or large variance is observed CHANGES IN VERSION 1.0.0 ------------------------- o first Bioconductor release CHANGES IN VERSION 0.99.0 (10-02-2019) ------------------------- o package submitted to Bioconductor CHANGES IN VERSION 0.9.10 (08-12-2019) ------------------------- o SAIGE algorithm implementation for quantitative outcomes CHANGES IN VERSION 0.9.9 (07-24-2019) ------------------------- o add a vignette to the package o the default of random number generator changes in R: "Rounding" was the default in `RNGkind()` prior to R_3.6.0, but "Rejection" is used in R (>= v3.6.0). For reproduction of the results created by R (< v3.6.0), please use `RNGkind("Mersenne-Twister", "Inversion", "Rounding")` in R (>= v3.6.0) CHANGES IN VERSION 0.9.7 (06-08-2019) ------------------------- o seqAssocGLMM_SPA(): load balancing in parallel CHANGES IN VERSION 0.9.0 (01-07-2019) ------------------------- o first version of SAIGEgds