version 0.36.3.1

0.36.3: Add option IsOutputBETASEinBurdenTest in step 2 to output effect sizes for burden tests.
0.36.3.1: update to use SPAtest v3.0.2

Allowing for customized weights for gene- or region- based tests

0.36.2: The option weights.beta.common is not fully correctly developed, so we make weights.beta.common equal to weights.beta.rare for now. Instead of output NA for SKAT-O p values when the function SKAT:::Met_SKAT_Get_Pvalue failed, output 2*min(SKAT p, Burden p, 0.5). allow for specifying customized weights for markers in gene- or region-based tests with arguments in step 2: weightsIncludeinGroupFile and weights_for_G2_cond

Accounting for case-control imbalance in conditional analysis for gene- or region-based tests

** Note: in v0.36.1, plain text dosage files are no longer allowed as input in step 2 to get rid of the dependence of the boost_iostream library

Bugs fixed: 1. fixed the freq calculation for mean impute for missing genotypes in plinkFile 2. Diagonal elements of GRM are now estimated using markers in plinkFile with MAF >= minMAFforGRM 3. Conditional analysis for gene- or region-based test for binary traits is now accounting for case-control imbalance 4. plain dosage files are no longer supported for step 2 so no external boost_iostream library is needed

** minMAFforGRM is added as a parameter in step 0 and 1, so only markers in the plinkFile with MAF >= minMAFforGRM will be used for GRM ** weights.beta.rare, weights.beta.common, weightMAFcutoff, dosageZerodCutoff, IsOutputPvalueNAinGroupTestforBinary, IsAccountforCasecontrolImbalanceinGroupTest are added as new parameters in step 2

Accounts for case-control imbalance in region/gene-based tests

0.35.8.8

Update README.md

v0.35.8.3

version 0.35.8.3

0.35.8.2

Single-variant(SAIGE) and gene-based(SAIGE-GENE) tests have been implemented in the same library

v0.29.5

version 0.29.5

Single-variant association test

Break loop for model fitting when tau2 is 0 for quantitative traits.
Solved the issue for the symlinks of the savvy library.