update DESCRIPTION for version 0.29.5

DESCRIPTION

@@ -2,16 +2,16 @@ Package: SAIGE
 Type: Package
 Title: Efficiently controlling for unbalanced case-control ratios and
         sample relatedness for binary traits in PheWAS by large cohorts
-Version: 0.29.4.4
-Date: 2018-12-18
+Version: 0.29.5
+Date: 2019-1-23
 Author: Wei Zhou, Seunggeun Lee, Cristen Willer
 Maintainer: Wei Zhou <[email protected]>
-Description: an R package that implements the Scalable and Accurate Implementation of Generalized mixed model that uses the saddlepoint approximation (SPA)(mhof, J. P. , 1961; Kuonen, D. 1999; Dey, R. et.al 2017) and large scale optimization techniques to calibrate case-control ratios in logistic mixed model score tests (Chen, H. et al. 2016) in large PheWAS. SAIGE can take dosage files in either bgen format and plain text format. Estimated effect sizes are provided. Support VCF,BCF and SAV as input format using the SAVVY library. QR decomposition for the covariate matrix. Allow models with no covariates. Allow using large number of genetic markers to construct GRM (e.g. > 600,000 markers). Fixed a Bug for the Tstat output. Use coefficent of variations for trace estimators and variane ratio estimation. Fixed a bug for colSums() when there is no covariate. BETA and Tstat are now for the alt allele for both quantitative and binary traits. Added an option for leave-one-chromosome-out (LOCO), cut off for the coefficient of variation for trace estimates and variance ratio estimates. Update the savvy library. Update SAIGE as SPAtest library is updated (bug fixed). A bug is fixed in the savvy library for vcf and sav format input. A bug is fixed for step 1 for binary traits, which may not affect much on step 1 results. Break when tau is 0 for quantitative traits in step 1
+Description: an R package that implements the Scalable and Accurate Implementation of Generalized mixed model that uses the saddlepoint approximation (SPA)(mhof, J. P. , 1961; Kuonen, D. 1999; Dey, R. et.al 2017) and large scale optimization techniques to calibrate case-control ratios in logistic mixed model score tests (Chen, H. et al. 2016) in large PheWAS. SAIGE can take dosage files in either bgen format and plain text format. Estimated effect sizes are provided. Support VCF,BCF and SAV as input format using the SAVVY library. QR decomposition for the covariate matrix. Allow models with no covariates. Allow using large number of genetic markers to construct GRM (e.g. > 600,000 markers). Fixed a Bug for the Tstat output. Use coefficent of variations for trace estimators and variane ratio estimation. Fixed a bug for colSums() when there is no covariate. BETA and Tstat are now for the alt allele for both quantitative and binary traits. Added an option for leave-one-chromosome-out (LOCO), cut off for the coefficient of variation for trace estimates and variance ratio estimates. Update the savvy library. Update SAIGE as SPAtest library is updated (bug fixed). A bug is fixed in the savvy library for vcf and sav format input. A bug is fixed for step 1 for binary traits, which may not affect much on step 1 results. Break when tau is 0 for quantitative traits in step 1. Add code to check sample size in sample file and dosage file
 License: GPL (>= 2)
 Imports: Rcpp (>= 0.12.12), RcppParallel, Matrix
 LinkingTo: Rcpp, RcppArmadillo, RcppParallel, data.table, SPAtest (== 3.0.0),
         RcppEigen, Matrix, methods
 SystemRequirements: GNU make
 RoxygenNote: 6.0.1
 NeedsCompilation: yes
-Packaged: 2018-08-21 05:44:37 UTC; zhowei
+Packaged: 2019-01-23 05:44:37 UTC; zhowei