MultiSTAAR v0.9.7.1

Author: xihaoli

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: MultiSTAAR
 Type: Package
 Title: Multi-Trait STAAR (MultiSTAAR) Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole-Genome Sequencing Studies
-Version: 0.9.7
-Date: 2024-10-19
+Version: 0.9.7.1
+Date: 2024-11-14
 Author: Xihao Li [aut, cre], Zilin Li [aut, cre], Han Chen [aut], Zhonghua Liu [aut]
 Maintainer: Xihao Li <xihaoli@unc.edu>, Zilin Li <lizl@nenu.edu.cn>
 Description: An R package for performing MultiSTAAR procedure in whole-genome sequencing studies.

R/Indiv_Score_Test_Region_multi.R

@@ -13,6 +13,8 @@
 #' 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 data frame with p rows corresponding to the p genetic variants in the given variant-set
 #' and (k+1) columns: \code{Score1},...,\code{Scorek} (the score test statistics for each phenotype)
 #' and \code{pvalue} (the multivariate score test p-value).
@@ -25,7 +27,8 @@
 #' @export
 
 Indiv_Score_Test_Region_multi <- function(genotype,obj_nullmodel,
-                                          rare_maf_cutoff=0.01,rv_num_cutoff=2){
+                                          rare_maf_cutoff=0.01,rv_num_cutoff=2,
+                                          rv_num_cutoff_max=1e9){
 
   if(class(genotype)[1] != "matrix" && !(!is.null(attr(class(genotype), "package")) && attr(class(genotype), "package") == "Matrix")){
     stop("genotype is not a matrix!")
@@ -49,6 +52,10 @@ Indiv_Score_Test_Region_multi <- function(genotype,obj_nullmodel,
   rm(genotype,MAF)
   gc()
 
+  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")
     G <- Diagonal(n = obj_nullmodel$n.pheno) %x% G

R/Indiv_Score_Test_Region_multi_cond.R

@@ -19,6 +19,8 @@
 #' 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;
@@ -40,6 +42,7 @@
 
 Indiv_Score_Test_Region_multi_cond <- function(genotype,genotype_adj,obj_nullmodel,
                                                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
@@ -73,6 +76,10 @@ Indiv_Score_Test_Region_multi_cond <- function(genotype,genotype_adj,obj_nullmod
   rm(genotype,MAF)
   gc()
 
+  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")
     G <- Diagonal(n = obj_nullmodel$n.pheno) %x% G

R/MultiSTAAR.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
@@ -85,7 +87,8 @@
 #' @export
 
 MultiSTAAR <- 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!")
@@ -112,6 +115,10 @@ MultiSTAAR <- 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")
     cMAC <- sum(G)

R/MultiSTAAR_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;
@@ -99,7 +101,7 @@
 #' @export
 
 MultiSTAAR_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
@@ -136,6 +138,10 @@ MultiSTAAR_cond <- function(genotype,genotype_adj,obj_nullmodel,annotation_phred
   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")
     cMAC <- sum(G)

README.md

@@ -29,7 +29,7 @@ Please see the <a href="docs/MultiSTAAR_manual.pdf">**MultiSTAAR** user manual</
 ## 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 (October 19, 2024).
+The current version is 0.9.7.1 (November 14, 2024).
 ## License
 This software is licensed under GPLv3.