1.0.9

Author: weizhouUMICH

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SAIGE
 Type: Package
 Title: Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE+) 
-Version: 1.0.8
-Date: 2022-05-13
+Version: 1.0.9
+Date: 2022-05-17
 Author: Wei Zhou, Zhangchen Zhao, Wenjian Bi, Seunggeun Lee, Cristen Willer
 Maintainer: SAIGE team <saige.genetics@gmail.com> 
 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. It conducts both single-variant association tests and set-based tests for rare variants.  
@@ -15,4 +15,4 @@ SystemRequirements: GNU make
 RoxygenNote: 7.1.2
 NeedsCompilation: yes
 Encoding: UTF-8
-Packaged: 2021-05-13 EST
+Packaged: 2021-05-17 EST

R/RcppExports.R

@@ -33,8 +33,8 @@ setVCFobjInCPP <- function(t_vcfFileName, t_vcfFileIndex, t_vcfField, t_SampleIn
     invisible(.Call('_SAIGE_setVCFobjInCPP', PACKAGE = 'SAIGE', t_vcfFileName, t_vcfFileIndex, t_vcfField, t_SampleInModel))
 }
 
-setSAIGEobjInCPP <- function(t_XVX, t_XXVX_inv, t_XV, t_XVX_inv_XV, t_X, t_S_a, t_res, t_mu2, t_mu, t_varRatio_sparse, t_varRatio_null, t_cateVarRatioMinMACVecExclude, t_cateVarRatioMaxMACVecInclude, t_SPA_Cutoff, t_tauvec, t_traitType, t_y, t_impute_method, t_flagSparseGRM, t_isFastTest, t_pval_cutoff_for_fastTest, t_locationMat, t_valueVec, t_dimNum, t_isCondition, t_condition_genoIndex, t_is_Firth_beta, t_pCutoffforFirth, t_offset) {
-    invisible(.Call('_SAIGE_setSAIGEobjInCPP', PACKAGE = 'SAIGE', t_XVX, t_XXVX_inv, t_XV, t_XVX_inv_XV, t_X, t_S_a, t_res, t_mu2, t_mu, t_varRatio_sparse, t_varRatio_null, t_cateVarRatioMinMACVecExclude, t_cateVarRatioMaxMACVecInclude, t_SPA_Cutoff, t_tauvec, t_traitType, t_y, t_impute_method, t_flagSparseGRM, t_isFastTest, t_pval_cutoff_for_fastTest, t_locationMat, t_valueVec, t_dimNum, t_isCondition, t_condition_genoIndex, t_is_Firth_beta, t_pCutoffforFirth, t_offset))
+setSAIGEobjInCPP <- function(t_XVX, t_XXVX_inv, t_XV, t_XVX_inv_XV, t_Sigma_iXXSigma_iX, t_X, t_S_a, t_res, t_mu2, t_mu, t_varRatio_sparse, t_varRatio_null, t_cateVarRatioMinMACVecExclude, t_cateVarRatioMaxMACVecInclude, t_SPA_Cutoff, t_tauvec, t_traitType, t_y, t_impute_method, t_flagSparseGRM, t_isFastTest, t_pval_cutoff_for_fastTest, t_locationMat, t_valueVec, t_dimNum, t_isCondition, t_condition_genoIndex, t_is_Firth_beta, t_pCutoffforFirth, t_offset) {
+    invisible(.Call('_SAIGE_setSAIGEobjInCPP', PACKAGE = 'SAIGE', t_XVX, t_XXVX_inv, t_XV, t_XVX_inv_XV, t_Sigma_iXXSigma_iX, t_X, t_S_a, t_res, t_mu2, t_mu, t_varRatio_sparse, t_varRatio_null, t_cateVarRatioMinMACVecExclude, t_cateVarRatioMaxMACVecInclude, t_SPA_Cutoff, t_tauvec, t_traitType, t_y, t_impute_method, t_flagSparseGRM, t_isFastTest, t_pval_cutoff_for_fastTest, t_locationMat, t_valueVec, t_dimNum, t_isCondition, t_condition_genoIndex, t_is_Firth_beta, t_pCutoffforFirth, t_offset))
 }
 
 setSparseSigmaInCPP <- function(r, t_locationMatinR, t_valueVecinR) {

extdata/input/group_new_chrposa1a2_emptychunk.txt

@@ -0,0 +1,10 @@
+GENE1 var 1:1:A:C 1:2:A:C 1:3:A:C 1:4:A:C 1:5:A:C 1:6:A:C 1:7:A:C 1:8:A:C 1:9:A:C 1:10:A:C 1:11:A:C 1:12:A:C 1:13:A:C 1:14:A:C 1:15:A:C 1:16:A:C 1:17:A:C 1:18:A:C 1:19:A:C 1:20:A:C 1:21:A:C 1:22:A:C 1:23:A:C 1:24:A:C 1:25:A:C 1:26:A:C 1:27:A:C 1:28:A:C 1:29:A:C 1:30:A:C 1:31:A:C 1:32:A:C 1:33:A:C 1:34:A:C 1:35:A:C 1:36:A:C 1:37:A:C 1:38:A:C 1:39:A:C 1:40:A:C 1:41:A:C 1:42:A:C 1:43:A:C 1:44:A:C 1:45:A:C 1:46:A:C 1:47:A:C 1:48:A:C 1:49:A:C 1:50:A:C
+GENE1 anno lof lof lof lof lof lof lof lof lof lof missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof
+GENE3 var 1:51:A:C
+GENE3 anno intergenic
+GENE4 var 1:1001:A:C
+GENE4 anno lof
+GENE2 var 1:51:A:C 1:52:A:C 1:53:A:C 1:54:A:C 1:55:A:C 1:56:A:C 1:57:A:C 1:58:A:C 1:59:A:C 1:60:A:C 1:61:A:C 1:62:A:C 1:63:A:C 1:64:A:C 1:65:A:C 1:66:A:C 1:67:A:C 1:68:A:C 1:69:A:C 1:70:A:C 1:71:A:C 1:72:A:C 1:73:A:C 1:74:A:C 1:75:A:C 1:76:A:C 1:77:A:C 1:78:A:C 1:79:A:C 1:80:A:C 1:81:A:C 1:82:A:C 1:83:A:C 1:84:A:C 1:85:A:C 1:86:A:C 1:87:A:C 1:88:A:C 1:89:A:C 1:90:A:C 1:91:A:C 1:92:A:C 1:93:A:C 1:94:A:C 1:95:A:C 1:96:A:C 1:97:A:C 1:98:A:C 1:99:A:C 1:100:A:C
+GENE2 anno missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense missense lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof lof
+GENE5 var 1:1099:A:C
+GENE5 anno lof

extdata/output/example_binary.rda

@@ -1 +1 @@
-0.9395061523359 null 1
+0.940221028361359 null 1

extdata/output/example_binary.varianceRatio.txt

@@ -1,4 +1,4 @@
-0.999319874008734 sparse 1
-0.941170368077863 null 1
-0.999204617103155 sparse 2
-0.941085399811388 null 2
+0.999412146820274 sparse 1
+0.94564842671888 null 1
+0.999153691613494 sparse 2
+0.939961135764744 null 2

extdata/output/example_binary_cate.varianceRatio.txt

@@ -1,4 +1,4 @@
-0.999319876424669 sparse 1
-0.941170379023014 null 1
-0.999204615537793 sparse 2
-0.941085410756765 null 2
+0.999412139663868 sparse 1
+0.945648350425262 null 1
+0.999153688084082 sparse 2
+0.939961056366588 null 2

extdata/output/example_binary_fullGRM.rda

@@ -1,4 +1,4 @@
-1 sparse 1
-0.948361740034301 null 1
-1 sparse 2
-0.943932314823564 null 2
+0.999994003566461 sparse 1
+0.948361988215753 null 1
+0.99999220284777 sparse 2
+0.943932580185106 null 2