NEWS

SAIGEgds 2.12.0

fix a C++ error that 'span' is ambiguous
new functions 'seqRefitNullGLMM()', 'seqAssocGLMM_GT()' and 'seqAssocGLMM_ACAT_O_GT()'
SAIGEgds supports optional OpenCL-based GPU acceleration for the GRM cross-product computation during null model fitting
new 'use.gpu' argument in 'seqFitSparseGRM()' and 'seqFitDenseGRM()' for OpenCL GPU-accelerated GRM construction
new 'geno.model' argument in 'seqAssocGLMM_SPA()', 'seqAssocGLMM_GT()', 'seqAssocGLMM_Burden()', 'seqAssocGLMM_SKAT()', 'seqAssocGLMM_ACAT_V()', 'seqAssocGLMM_ACAT_O()' and 'seqAssocGLMM_ACAT_O_GT()' for additive, dominant, or recessive genetic models

'fork.loading' is deprecated in ‘seqFitNullGLMM_SPA()', use ’parallel.loading' instead

improve the work load balancing in 'seqAssocGLMM_SPA()' according to SeqArray_1.49.6
new option 'verbose.pval' to improve the display in 'seqAssocGLMM_SPA()'

update 'seqFitLDpruning()'
reduce the memory usage in 'seqAssocGLMM_SPA()' when the genotype file is not split by chromosomes

fix the "Matrix-deprecated" warning from the Matrix package when calling 'as(dsCMatrix, "dgCMatrix")'

New features to use sparse genetic relationship matrix in generalized linear mixed models (GLMMs) according to the SAIGE-GENE paper (Zhou et al., 2020)
a new argument 'grm.mat' in ‘seqFitNullGLMM_SPA()': the dense or sparse genetic relationship matrix (GRM) can be specified via ’grm.mat'
MAC categories for multiple variance ratios in 'seqFitNullGLMM_SPA()', 'seqAssocGLMM_SPA()', designed for rare variants
new function 'seqAssocGLMM_SKAT()' for the SKAT aggregate method
new feature 'seqAssocGLMM_ACAT_O()' to include the SKAT aggregate method for full ACAT-O tests
faster 'seqSAIGE_LoadPval()' when merging multiple input files

fix the compiling issue on ARM64 (see https://github.com/AbbVie-ComputationalGenomics/SAIGEgds/issues/8)

fix the memory issue because of using deprecated tbb::task_scheduler_init in RcppParallel

'seqFitNullGLMM_SPA()' can use imputed dosages directly without converting the dosages to the best-guess genotypes
new function 'glmmHeritability()' for approximate heritability estimates

add a new option for the threshold of missing variant to 'seqAssocGLMM_SPA()'
change the output column 'AC.alt' to 'mac' in 'seqAssocGLMM_SPA()'
retry model fitting at least 10 times if matrix is singular or not positive definite, or large variance is observed

add a vignette to the package
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)