STAARpipeline v0.9.7

R/fit_nullmodel.R

@@ -83,11 +83,14 @@ fit_nullmodel <- function(fixed, data = parent.frame(), kins, use_sparse = NULL,
 		if(use_SPA)
 		{
 			# generate XW
-			X <- model.matrix(obj_nullmodel)
+			X <- obj_nullmodel$X
 			working <- obj_nullmodel$weights
 
-			obj_nullmodel$XW <- t(X)%*%diag(working)
-			obj_nullmodel$XXWX_inv <- X%*%solve(t(X)%*%diag(working)%*%X)
+			obj_nullmodel$XW <- as.matrix(crossprod(X,obj_nullmodel$Sigma_i))
+			obj_nullmodel$XXWX_inv <- as.matrix(X%*%obj_nullmodel$cov)
+
+			obj_nullmodel$XSigma_i <- obj_nullmodel$XW
+			obj_nullmodel$XXSigma_iX_inv <- obj_nullmodel$XXWX_inv
 		}
 
 	}else if(!inherits(kins, "matrix") && !inherits(kins, "Matrix")){
@@ -147,11 +150,10 @@ fit_nullmodel <- function(fixed, data = parent.frame(), kins, use_sparse = NULL,
 
 		if(use_SPA)
 		{
-			X <- model.matrix(obj_nullmodel)
-			working <- obj_nullmodel$weights
+			X <- obj_nullmodel$X
 
-			obj_nullmodel$XW <- t(X)%*%diag(working)
-			obj_nullmodel$XXWX_inv <- X%*%solve(t(X)%*%diag(working)%*%X)
+			obj_nullmodel$XW <- as.matrix(crossprod(X,obj_nullmodel$Sigma_i))
+			obj_nullmodel$XXWX_inv <- as.matrix(X%*%obj_nullmodel$cov)
 		}
 	}
 	obj_nullmodel$relatedness <- TRUE

README.md

@@ -32,7 +32,7 @@ Please see the <a href="docs/STAARpipeline_manual.pdf">**STAARpipeline** user ma
 ## Data Availability
 The whole-genome functional annotation data assembled from a variety of sources and the precomputed annotation principal components are available at the [Functional Annotation of Variant - Online Resource (FAVOR)](https://favor.genohub.org) site and [FAVOR Essential Database](https://doi.org/10.7910/DVN/1VGTJI).
 ## Version
-The current version is 0.9.7 (November 9, 2023).
+The current version is 0.9.7 (January 22, 2024).
 ## Citation
 If you use **STAARpipeline** and **STAARpipelineSummary** for your work, please cite: