NEWS

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SAIGEgds 2.4.1

• add an option 'load.balancing' to 'seqAssocGLMM_SPA()'

SAIGEgds 2.4.0

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

SAIGEgds 2.2.1

• fix the compiler warning: -Wformat-security
• fix a compiler issue with gcc v7.5

SAIGEgds 2.2.0

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

SAIGEgds 2.0.0

NEW FEATURES

• 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

SAIGEgds 1.12.5

• enable RCPP_PARALLEL_USE_TBB=1 on Windows

SAIGEgds 1.12.4

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

SAIGEgds 1.12.1

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

SAIGEgds 1.6.0

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

SAIGEgds 1.4.0

• set-based tests: burden, ACAT-V

SAIGEgds 1.2.2

• update the citation
• work around gcc-10

SAIGEgds 1.2.0

• 'seqAssocGLMM_SPA()' can save to a RDS file

SAIGEgds 1.0.2

• fix an issue when there is no covariate in the formula (e.g., y ~ 1)

SAIGEgds 1.0.1

• 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

SAIGEgds 1.0.0

• first Bioconductor release

SAIGEgds 0.99.0

• package submitted to Bioconductor

SAIGEgds 0.9.10

• SAIGE algorithm implementation for quantitative outcomes

SAIGEgds 0.9.9

• 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)

SAIGEgds 0.9.7

• seqAssocGLMM_SPA(): load balancing in parallel

SAIGEgds 0.9.0

• first version of SAIGEgds