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weizhouUMICH committed May 18, 2022
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6 changes: 3 additions & 3 deletions DESCRIPTION
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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 <[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. It conducts both single-variant association tests and set-based tests for rare variants.
Expand All @@ -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
4 changes: 2 additions & 2 deletions R/RcppExports.R
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Expand Up @@ -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) {
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10 changes: 10 additions & 0 deletions extdata/input/group_new_chrposa1a2_emptychunk.txt
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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
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0.9395061523359 null 1
0.940221028361359 null 1
8 changes: 4 additions & 4 deletions extdata/output/example_binary_cate.varianceRatio.txt
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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
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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
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8 changes: 4 additions & 4 deletions extdata/output/example_binary_sparseGRM.varianceRatio.txt
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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
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1 sparse 1
0.943886958308967 null 1
0.999992932317471 sparse 1
0.943887223195798 null 1
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1.22260160693625 null 1
1.22420115246319 null 1
15 changes: 15 additions & 0 deletions extdata/output/genotype_100markers_bgen_groupTest_out.txt
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Region Group max_MAF Pvalue Pvalue_Burden Pvalue_SKAT BETA_Burden SE_Burden MAC MAC_case MAC_control Number_rare Number_ultra_rare
GENE1 lof 0.001 0.0284103409315078 0.0284103409315078 0.0284103409315078 0.146466637563443 0.0668317350724161 5 2 3 0 4
GENE1 lof 0.01 0.461873043542753 0.312404313255535 0.844692146977405 -0.0206968895195961 0.0204881174799804 98 7 91 3 12
GENE1 missense;lof 0.001 0.0632430428041422 0.0632430428041422 0.0632430428041422 0.0897047539703816 0.0482938198596467 10 3 7 0 7
GENE1 missense;lof 0.01 0.546427994680353 0.373144949649244 0.939528567390847 -0.0160032993323661 0.0179691644420352 119 10 109 4 17
GENE1 missense;lof;synonymous 0.001 0.0632430428041422 0.0632430428041422 0.0632430428041422 0.0897047539703816 0.0482938198596467 10 3 7 0 7
GENE1 missense;lof;synonymous 0.01 0.546427994680353 0.373144949649244 0.939528567390847 -0.0160032993323661 0.0179691644420352 119 10 109 4 17
GENE1 Cauchy NA 0.0888496037371469 0.082537293113971 0.190100028209205 NA NA NA NA NA NA NA
GENE2 lof 0.001 0.437270497979142 0.437270497979142 0.437270497979142 -0.0503519823411405 0.0648188628035735 5 0 5 0 3
GENE2 lof 0.01 0.637283777438903 0.950580303523347 0.502025417630713 -0.00211339925455253 0.0340991511290716 22 2 20 1 4
GENE2 missense;lof 0.001 0.956929357643779 0.956929357643779 0.956929357643779 0.00211302169047503 0.0391247508309761 15 2 13 0 9
GENE2 missense;lof 0.01 0.610540847559672 0.437149329837039 0.719626679341351 0.0166609896475776 0.021442273543376 77 10 67 3 15
GENE2 missense;lof;synonymous 0.001 0.956929357643779 0.956929357643779 0.956929357643779 0.00211302169047503 0.0391247508309761 15 2 13 0 9
GENE2 missense;lof;synonymous 0.01 0.610540847559672 0.437149329837039 0.719626679341351 0.0166609896475776 0.021442273543376 77 10 67 3 15
GENE2 Cauchy NA 0.883634981392914 0.909283061098184 0.886758740586464 NA NA NA NA NA NA NA
14 changes: 12 additions & 2 deletions extdata/output/genotype_100markers_bgen_groupTest_out.txt.markerList.txt
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Region Group max_MAF Rare_Variants Ultra_Rare_Variants
GENE1 lof 0.5 1:4:A:C,1:31:A:C,1:33:A:C,1:37:A:C,1:38:A:C,1:48:A:C,1:50:A:C 1:3:A:C,1:8:A:C,1:9:A:C,1:10:A:C,1:32:A:C,1:34:A:C,1:35:A:C,1:42:A:C,1:44:A:C,1:45:A:C,1:46:A:C,1:49:A:C
GENE2 lof 0.5 1:81:A:C,1:83:A:C,1:86:A:C,1:90:A:C,1:91:A:C,1:92:A:C,1:94:A:C,1:96:A:C,1:97:A:C,1:99:A:C 1:84:A:C,1:85:A:C,1:89:A:C,1:98:A:C
GENE1 lof 0.001 1:3:A:C,1:32:A:C,1:42:A:C,1:44:A:C
GENE1 lof 0.01 1:4:A:C,1:31:A:C,1:33:A:C 1:3:A:C,1:8:A:C,1:9:A:C,1:10:A:C,1:32:A:C,1:34:A:C,1:35:A:C,1:42:A:C,1:44:A:C,1:45:A:C,1:46:A:C,1:49:A:C
GENE1 missense;lof 0.001 1:3:A:C,1:11:A:C,1:13:A:C,1:28:A:C,1:32:A:C,1:42:A:C,1:44:A:C
GENE1 missense;lof 0.01 1:4:A:C,1:17:A:C,1:31:A:C,1:33:A:C 1:3:A:C,1:8:A:C,1:9:A:C,1:10:A:C,1:11:A:C,1:13:A:C,1:16:A:C,1:18:A:C,1:28:A:C,1:32:A:C,1:34:A:C,1:35:A:C,1:42:A:C,1:44:A:C,1:45:A:C,1:46:A:C,1:49:A:C
GENE1 missense;lof;synonymous 0.001 1:3:A:C,1:11:A:C,1:13:A:C,1:28:A:C,1:32:A:C,1:42:A:C,1:44:A:C
GENE1 missense;lof;synonymous 0.01 1:4:A:C,1:17:A:C,1:31:A:C,1:33:A:C 1:3:A:C,1:8:A:C,1:9:A:C,1:10:A:C,1:11:A:C,1:13:A:C,1:16:A:C,1:18:A:C,1:28:A:C,1:32:A:C,1:34:A:C,1:35:A:C,1:42:A:C,1:44:A:C,1:45:A:C,1:46:A:C,1:49:A:C
GENE2 lof 0.001 1:84:A:C,1:85:A:C,1:89:A:C
GENE2 lof 0.01 1:91:A:C 1:84:A:C,1:85:A:C,1:89:A:C,1:98:A:C
GENE2 missense;lof 0.001 1:55:A:C,1:56:A:C,1:62:A:C,1:76:A:C,1:77:A:C,1:78:A:C,1:84:A:C,1:85:A:C,1:89:A:C
GENE2 missense;lof 0.01 1:60:A:C,1:70:A:C,1:91:A:C 1:55:A:C,1:56:A:C,1:58:A:C,1:61:A:C,1:62:A:C,1:65:A:C,1:72:A:C,1:74:A:C,1:76:A:C,1:77:A:C,1:78:A:C,1:84:A:C,1:85:A:C,1:89:A:C,1:98:A:C
GENE2 missense;lof;synonymous 0.001 1:55:A:C,1:56:A:C,1:62:A:C,1:76:A:C,1:77:A:C,1:78:A:C,1:84:A:C,1:85:A:C,1:89:A:C
GENE2 missense;lof;synonymous 0.01 1:60:A:C,1:70:A:C,1:91:A:C 1:55:A:C,1:56:A:C,1:58:A:C,1:61:A:C,1:62:A:C,1:65:A:C,1:72:A:C,1:74:A:C,1:76:A:C,1:77:A:C,1:78:A:C,1:84:A:C,1:85:A:C,1:89:A:C,1:98:A:C
19 changes: 19 additions & 0 deletions extdata/output/genotype_100markers_bgen_groupTest_out.txt.singleAssoc.txt
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CHR POS MarkerID Allele1 Allele2 AC_Allele2 AF_Allele2 MissingRate BETA SE Tstat var p.value p.value.NA Is.SPA AF_case AF_ctrl N_case N_ctrl
1 4 rs4 A C 20 0.01 0 -0.0661039 0.790161 -0.105876 1.60165 0.933328 0.933328 false 0.0102041 0.00997783 98 902
1 17 rs17 A C 12 0.006 0 -0.0542031 0.830933 -0.0785041 1.44833 0.94799 0.94799 false 0.0102041 0.00554324 98 902
1 31 rs31 A C 16 0.008 0 -1.168 1.07019 -1.01981 0.873125 0.275099 0.275099 false 0 0.00886918 98 902
1 33 rs33 A C 17 0.0085 0 -0.406973 0.913755 -0.487423 1.19768 0.656042 0.656042 false 0.00510204 0.00886918 98 902
UR UR GENE1:lof:0.001 UR UR 5 0.0025 0 3.56297 1.59615 1.39291 0.390941 0.0256002 0.0258967 true 0.0102041 0.00166297 98 902
UR UR GENE1:lof:0.01 UR UR 45 0.0225 0 -0.309086 0.524336 -1.12424 3.63731 0.555539 0.555539 false 0.0204082 0.0227273 98 902
UR UR GENE1:missense;lof:0.001 UR UR 10 0.005 0 2.11543 1.10416 1.73516 0.820236 0.05538 0.05538 false 0.0153061 0.00388027 98 902
UR UR GENE1:missense;lof:0.01 UR UR 54 0.027 0 -0.254553 0.481809 -1.09655 4.30775 0.597272 0.597272 false 0.0255102 0.0271619 98 902
UR UR GENE1:missense;lof;synonymous:0.001 UR UR 10 0.005 0 2.11543 1.10416 1.73516 0.820236 0.05538 0.05538 false 0.0153061 0.00388027 98 902
UR UR GENE1:missense;lof;synonymous:0.01 UR UR 54 0.027 0 -0.254553 0.481809 -1.09655 4.30775 0.597272 0.597272 false 0.0255102 0.0271619 98 902
1 60 rs60 A C 11 0.0055 0 1.21856 0.947614 1.35701 1.11362 0.19847 0.19847 false 0.0153061 0.00443459 98 902
1 70 rs70 A C 12 0.006 0 -0.130679 1.0458 -0.119483 0.914323 0.900559 0.900559 false 0.00510204 0.00609756 98 902
1 91 rs91 A C 13 0.0065 0 0.737817 1.00539 0.729926 0.989304 0.463034 0.463034 false 0.0102041 0.00609756 98 902
UR UR GENE2:lof:0.001 UR UR 5 0.0025 0 -1.25354 1.56923 -0.509054 0.406095 0.424393 0.424393 false 0 0.00277162 98 902
UR UR GENE2:lof:0.01 UR UR 9 0.0045 0 -1.23471 1.26473 -0.771918 0.62518 0.328933 0.328933 false 0 0.00498891 98 902
UR UR GENE2:missense;lof:0.001 UR UR 15 0.0075 0 0.046628 0.839574 0.0661498 1.41867 0.95571 0.95571 false 0.0102041 0.00720621 98 902
UR UR GENE2:missense;lof:0.01 UR UR 41 0.0205 0 -0.108027 0.567597 -0.335313 3.10398 0.849056 0.849056 false 0.0204082 0.02051 98 902
UR UR GENE2:missense;lof;synonymous:0.001 UR UR 15 0.0075 0 0.046628 0.839574 0.0661498 1.41867 0.95571 0.95571 false 0.0102041 0.00720621 98 902
UR UR GENE2:missense;lof;synonymous:0.01 UR UR 41 0.0205 0 -0.108027 0.567597 -0.335313 3.10398 0.849056 0.849056 false 0.0204082 0.02051 98 902
18 changes: 9 additions & 9 deletions extdata/output/genotype_100markers_bgen_groupTest_out.txt.singleAssoc.txt_temp
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1 60 rs60 A C 11 0.0055 0 1.20485 0.943525 1.3534 1.12329 0.201613 0.201613 false 0.0153061 0.00443459 98 902
1 70 rs70 A C 12 0.006 0 -0.12552 1.04413 -0.115133 0.917251 0.904313 0.904313 false 0.00510204 0.00609756 98 902
1 91 rs91 A C 13 0.0065 0 0.73828 1.00308 0.73375 0.993864 0.461724 0.461724 false 0.0102041 0.00609756 98 902
UR UR GENE2:lof:0.001 UR UR 5 0.0025 0 -1.24447 1.56238 -0.509815 0.409665 0.425728 0.425728 false 0 0.00277162 98 902
UR UR GENE2:lof:0.01 UR UR 9 0.0045 0 -1.22607 1.26039 -0.771801 0.62949 0.330667 0.330667 false 0 0.00498891 98 902
UR UR GENE2:missense;lof:0.001 UR UR 15 0.0075 0 0.0433198 0.835695 0.0620284 1.43187 0.958659 0.958659 false 0.0102041 0.00720621 98 902
UR UR GENE2:missense;lof:0.01 UR UR 41 0.0205 0 -0.10736 0.566494 -0.334542 3.11609 0.849688 0.849688 false 0.0204082 0.02051 98 902
UR UR GENE2:missense;lof;synonymous:0.001 UR UR 15 0.0075 0 0.0433198 0.835695 0.0620284 1.43187 0.958659 0.958659 false 0.0102041 0.00720621 98 902
UR UR GENE2:missense;lof;synonymous:0.01 UR UR 41 0.0205 0 -0.10736 0.566494 -0.334542 3.11609 0.849688 0.849688 false 0.0204082 0.02051 98 902
1 60 rs60 A C 11 0.0055 0 1.21856 0.947614 1.35701 1.11362 0.19847 0.19847 false 0.0153061 0.00443459 98 902
1 70 rs70 A C 12 0.006 0 -0.130679 1.0458 -0.119483 0.914323 0.900559 0.900559 false 0.00510204 0.00609756 98 902
1 91 rs91 A C 13 0.0065 0 0.737817 1.00539 0.729926 0.989304 0.463034 0.463034 false 0.0102041 0.00609756 98 902
UR UR GENE2:lof:0.001 UR UR 5 0.0025 0 -1.25354 1.56923 -0.509054 0.406095 0.424393 0.424393 false 0 0.00277162 98 902
UR UR GENE2:lof:0.01 UR UR 9 0.0045 0 -1.23471 1.26473 -0.771918 0.62518 0.328933 0.328933 false 0 0.00498891 98 902
UR UR GENE2:missense;lof:0.001 UR UR 15 0.0075 0 0.046628 0.839574 0.0661498 1.41867 0.95571 0.95571 false 0.0102041 0.00720621 98 902
UR UR GENE2:missense;lof:0.01 UR UR 41 0.0205 0 -0.108027 0.567597 -0.335313 3.10398 0.849056 0.849056 false 0.0204082 0.02051 98 902
UR UR GENE2:missense;lof;synonymous:0.001 UR UR 15 0.0075 0 0.046628 0.839574 0.0661498 1.41867 0.95571 0.95571 false 0.0102041 0.00720621 98 902
UR UR GENE2:missense;lof;synonymous:0.01 UR UR 41 0.0205 0 -0.108027 0.567597 -0.335313 3.10398 0.849056 0.849056 false 0.0204082 0.02051 98 902
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