STAAR v0.9.7.2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: STAAR
 Type: Package
 Title: STAAR Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole-Genome Sequencing Studies
-Version: 0.9.7.1
-Date: 2024-08-09
+Version: 0.9.7.2
+Date: 2024-11-14
 Author: Xihao Li [aut, cre], Zilin Li [aut, cre], Han Chen [aut]
 Maintainer: Xihao Li <xihaoli@unc.edu>, Zilin Li <lizl@nenu.edu.cn>
 Description: An R package for performing STAAR procedure in whole-genome sequencing studies.

R/STAAR.R

@@ -25,6 +25,8 @@
 #' defining rare variants (default = 0.01).
 #' @param rv_num_cutoff the cutoff of minimum number of variants of analyzing
 #' a given variant-set (default = 2).
+#' @param rv_num_cutoff_max the cutoff of maximum number of variants of analyzing
+#' a given variant-set (default = 1e+09).
 #' @return A list with the following members:
 #' @return \code{num_variant}: the number of variants with minor allele frequency > 0 and less than
 #' \code{rare_maf_cutoff} in the given variant-set that are used for performing the
@@ -81,7 +83,8 @@
 #' @export
 
 STAAR <- function(genotype,obj_nullmodel,annotation_phred=NULL,
-                  rare_maf_cutoff=0.01,rv_num_cutoff=2){
+                  rare_maf_cutoff=0.01,rv_num_cutoff=2,
+                  rv_num_cutoff_max=1e9){
 
   if(!inherits(genotype, "matrix") && !inherits(genotype, "Matrix")){
     stop("genotype is not a matrix!")
@@ -108,6 +111,10 @@ STAAR <- function(genotype,obj_nullmodel,annotation_phred=NULL,
   gc()
   annotation_phred <- annotation_phred[RV_label,,drop=FALSE]
 
+  if(sum(RV_label) >= rv_num_cutoff_max){
+    stop(paste0("Number of rare variant in the set is more than ",rv_num_cutoff_max,"!"))
+  }
+
   if(sum(RV_label) >= rv_num_cutoff){
     G <- as(Geno_rare,"dgCMatrix")
     MAF <- MAF[RV_label]

R/STAAR_Binary_SPA.R

@@ -23,6 +23,8 @@
 #' defining rare variants (default = 0.01).
 #' @param rv_num_cutoff the cutoff of minimum number of variants of analyzing
 #' a given variant-set (default = 2).
+#' @param rv_num_cutoff_max the cutoff of maximum number of variants of analyzing
+#' a given variant-set (default = 1e+09).
 #' @param tol a positive number specifying tolerance, the difference threshold for parameter
 #' estimates in saddlepoint apporximation algorithm below which iterations should be stopped (default = ".Machine$double.eps^0.25").
 #' @param max_iter a positive integers pecifying the maximum number of iterations for applying the saddlepoint approximation algorithm (default = "1000").
@@ -66,6 +68,7 @@
 
 STAAR_Binary_SPA <- function(genotype,obj_nullmodel,annotation_phred=NULL,
                              rare_maf_cutoff=0.01,rv_num_cutoff=2,
+                             rv_num_cutoff_max=1e9,
                              tol=.Machine$double.eps^0.25,max_iter=1000,
                              SPA_p_filter=FALSE,p_filter_cutoff=0.05){
 
@@ -95,6 +98,10 @@ STAAR_Binary_SPA <- function(genotype,obj_nullmodel,annotation_phred=NULL,
   # gc()
   annotation_phred <- annotation_phred[RV_label,,drop=FALSE]
 
+  if(sum(RV_label) >= rv_num_cutoff_max){
+    stop(paste0("Number of rare variant in the set is more than ",rv_num_cutoff_max,"!"))
+  }
+
   if(sum(RV_label) >= rv_num_cutoff){
     # G <- as(Geno_rare,"dgCMatrix")
     MAF <- MAF[RV_label]

R/STAAR_cond.R

@@ -31,6 +31,8 @@
 #' defining rare variants (default = 0.01).
 #' @param rv_num_cutoff the cutoff of minimum number of variants of analyzing
 #' a given variant-set (default = 2).
+#' @param rv_num_cutoff_max the cutoff of maximum number of variants of analyzing
+#' a given variant-set (default = 1e+09).
 #' @param method_cond a character value indicating the method for conditional analysis.
 #' \code{optimal} refers to regressing residuals from the null model on \code{genotype_adj}
 #' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals;
@@ -95,7 +97,7 @@
 #' @export
 
 STAAR_cond <- function(genotype,genotype_adj,obj_nullmodel,annotation_phred=NULL,
-                       rare_maf_cutoff=0.01,rv_num_cutoff=2,
+                       rare_maf_cutoff=0.01,rv_num_cutoff=2,rv_num_cutoff_max=1e9,
                        method_cond=c("optimal","naive")){
 
   method_cond <- match.arg(method_cond) # evaluate choices
@@ -132,6 +134,10 @@ STAAR_cond <- function(genotype,genotype_adj,obj_nullmodel,annotation_phred=NULL
   gc()
   annotation_phred <- annotation_phred[RV_label,,drop=FALSE]
 
+  if(sum(RV_label) >= rv_num_cutoff_max){
+    stop(paste0("Number of rare variant in the set is more than ",rv_num_cutoff_max,"!"))
+  }
+
   if(sum(RV_label) >= rv_num_cutoff){
     G <- as(Geno_rare,"dgCMatrix")
     MAF <- MAF[RV_label]

README.md

@@ -29,7 +29,7 @@ Please see the <a href="docs/STAAR_manual.pdf">**STAAR** user manual</a> for det
 ## 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 0.9.7.1 (August 9, 2024).
+The current version is 0.9.7.2 (November 14, 2024).
 ## Citation
 If you use **STAAR** for your work, please cite: