MetaSTAAR v0.9.6.3

.github/workflows/R-CMD-check.yaml

@@ -11,7 +11,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: 4.3.0
+          r-version: 4.2.3
       - name: Install BiocManager
         run: |
           if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

.travis.yml

@@ -7,21 +7,12 @@ branches:
 language: r
 r:
   - 4.1.2
-
-before_install:
-  - mkdir -p ~/.R
-  - echo 'CXX17 = g++-7 -std=gnu++17 -fPIC' > ~/.R/Makevars
-  - while travis_wait 50 sleep 300 &> /tmp/build.log || (tail -n 100 /tmp/build.log && exit 1); do echo "=====[ $SECONDS seconds, buildroot still building... ]====="; done
-
-addons:
-  apt:
-    sources:
-      - sourceline: 'ppa:ubuntu-toolchain-r/test'
-    packages:
-      - g++-7
 
 warnings_are_errors: false
 
+r_binary_packages:
+- glmnet
+
 bioc_packages:
 - GENESIS
 

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: MetaSTAAR
 Type: Package
 Title: Meta-Analysis of STAAR (MetaSTAAR) Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole Genome Sequencing Studies
-Version: 0.9.6.2
-Date: 2023-07-05
+Version: 0.9.6.3
+Date: 2023-11-18
 Author: Xihao Li [aut, cre], Zilin Li [aut, cre], Corbin Quick [aut]
-Maintainer: Xihao Li <xihaoli@g.harvard.edu>, Zilin Li <[email protected].edu>
+Maintainer: Xihao Li <xihaoli@unc.edu>, Zilin Li <[email protected].edu>
 Description: An R package for performing MetaSTAAR procedure in whole genome sequencing studies.
 License: GPL-3
 Copyright: See COPYRIGHTS for details.

R/MetaSTAAR_individual_analysis.R

@@ -46,10 +46,7 @@ MetaSTAAR_individual_analysis <- function(chr,start.loc,end.loc,study.names,samp
   if (end.loc <= segment * segment.size) {
     ### summary statistics
     sumstat.files <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list <- lapply(sumstat.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list <- sapply(sumstat.files, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list <- lapply(sumstat.list, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)

R/MetaSTAAR_merge.R

@@ -54,10 +54,7 @@ MetaSTAAR_merge <- function(chr,start.loc,end.loc,study.names,sample.sizes,sumst
   if (end.loc <= segment * segment.size) {
     ### summary statistics
     sumstat.files <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list <- lapply(sumstat.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list <- sapply(sumstat.files, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list <- lapply(sumstat.list, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -113,10 +110,7 @@ MetaSTAAR_merge <- function(chr,start.loc,end.loc,study.names,sample.sizes,sumst
 
     ### covariance matrices
     cov.files <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    cov.list <- lapply(cov.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list <- sapply(cov.files, function(x) mget(load(x)), simplify = TRUE)
     cov.list <- lapply(cov.list, function(x) {
       if (is.null(x)) {
         as(matrix(nrow=0,ncol=0),"dgCMatrix")
@@ -147,10 +141,7 @@ MetaSTAAR_merge <- function(chr,start.loc,end.loc,study.names,sample.sizes,sumst
   }else if (end.loc <= (segment + 1) * segment.size) {
     ### summary statistics
     sumstat.files1 <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list1 <- lapply(sumstat.files1, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list1 <- sapply(sumstat.files1, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list1 <- lapply(sumstat.list1, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -169,10 +160,7 @@ MetaSTAAR_merge <- function(chr,start.loc,end.loc,study.names,sample.sizes,sumst
     }, x = sumstat.list1, y = cov_maf_cutoff, SIMPLIFY = FALSE)
 
     sumstat.files2 <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment+1,".Rdata")
-    sumstat.list2 <- lapply(sumstat.files2, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list2 <- sapply(sumstat.files2, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list2 <- lapply(sumstat.list2, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -247,10 +235,7 @@ MetaSTAAR_merge <- function(chr,start.loc,end.loc,study.names,sample.sizes,sumst
 
     ### covariance matrices
     cov.files1 <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    cov.list1 <- lapply(cov.files1, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list1 <- sapply(cov.files1, function(x) mget(load(x)), simplify = TRUE)
     cov.list1 <- mapply(function(x,y,z) {
       if (is.null(x)) {
         x <- as(matrix(nrow=length(y),ncol=(length(y)+length(z))),"dgCMatrix")
@@ -259,10 +244,7 @@ MetaSTAAR_merge <- function(chr,start.loc,end.loc,study.names,sample.sizes,sumst
     }, x = cov.list1, y = position.index1, z = position.index2, SIMPLIFY = FALSE)
 
     cov.files2 <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment+1,".Rdata")
-    cov.list2 <- lapply(cov.files2, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list2 <- sapply(cov.files2, function(x) mget(load(x)), simplify = TRUE)
     cov.list2 <- lapply(cov.list2, function(x) {
       if (is.null(x)) {
         as(matrix(nrow=0,ncol=0),"dgCMatrix")

R/MetaSTAAR_merge_cond.R

@@ -66,10 +66,7 @@ MetaSTAAR_merge_cond <- function(chr,start.loc,end.loc,study.names,sample.sizes,
   if (end.loc <= segment * segment.size) {
     ### summary statistics
     sumstat.files <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list <- lapply(sumstat.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list <- sapply(sumstat.files, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list <- lapply(sumstat.list, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -125,10 +122,7 @@ MetaSTAAR_merge_cond <- function(chr,start.loc,end.loc,study.names,sample.sizes,
 
     ### covariance matrices
     cov.files <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    cov.list <- lapply(cov.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list <- sapply(cov.files, function(x) mget(load(x)), simplify = TRUE)
     cov.list <- lapply(cov.list, function(x) {
       if (is.null(x)) {
         as(matrix(nrow=0,ncol=0),"dgCMatrix")
@@ -159,10 +153,7 @@ MetaSTAAR_merge_cond <- function(chr,start.loc,end.loc,study.names,sample.sizes,
   }else if (end.loc <= (segment + 1) * segment.size) {
     ### summary statistics
     sumstat.files1 <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list1 <- lapply(sumstat.files1, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list1 <- sapply(sumstat.files1, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list1 <- lapply(sumstat.list1, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -181,10 +172,7 @@ MetaSTAAR_merge_cond <- function(chr,start.loc,end.loc,study.names,sample.sizes,
     }, x = sumstat.list1, y = cov_maf_cutoff, SIMPLIFY = FALSE)
 
     sumstat.files2 <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment+1,".Rdata")
-    sumstat.list2 <- lapply(sumstat.files2, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list2 <- sapply(sumstat.files2, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list2 <- lapply(sumstat.list2, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -259,10 +247,7 @@ MetaSTAAR_merge_cond <- function(chr,start.loc,end.loc,study.names,sample.sizes,
 
     ### covariance matrices
     cov.files1 <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    cov.list1 <- lapply(cov.files1, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list1 <- sapply(cov.files1, function(x) mget(load(x)), simplify = TRUE)
     cov.list1 <- mapply(function(x,y,z) {
       if (is.null(x)) {
         x <- as(matrix(nrow=length(y),ncol=(length(y)+length(z))),"dgCMatrix")
@@ -271,10 +256,7 @@ MetaSTAAR_merge_cond <- function(chr,start.loc,end.loc,study.names,sample.sizes,
     }, x = cov.list1, y = position.index1, z = position.index2, SIMPLIFY = FALSE)
 
     cov.files2 <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment+1,".Rdata")
-    cov.list2 <- lapply(cov.files2, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list2 <- sapply(cov.files2, function(x) mget(load(x)), simplify = TRUE)
     cov.list2 <- lapply(cov.list2, function(x) {
       if (is.null(x)) {
         as(matrix(nrow=0,ncol=0),"dgCMatrix")
@@ -326,10 +308,7 @@ MetaSTAAR_merge_cond <- function(chr,start.loc,end.loc,study.names,sample.sizes,
 
   ### covariance files for conditional analysis
   covcond.files <- paste0(covcond.dir,"/cov.cond.",trait,".",study.names,".chr",chr,".region.",region,".Rdata")
-  covcond.list <- lapply(covcond.files, function(x) {
-    load(file = x)
-    get(ls()[ls()!= "cov.cond"])
-  })
+  covcond.list <- sapply(covcond.files, function(x) mget(load(x)), simplify = TRUE)
   variant_info_list <- lapply(covcond.list, function(x) {x$variant_info})
   variant_info_merge <- do.call("rbind",variant_info_list)
   variant_info_nodup <- variant_info_merge[!duplicated(variant_info_merge),]

R/MetaSTAAR_merge_varlist.R

@@ -55,10 +55,7 @@ MetaSTAAR_merge_varlist <- function(chr,variant_pos,study.names,sample.sizes,sum
   if (max(variant_pos) <= segment * segment.size) {
     ### summary statistics
     sumstat.files <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list <- lapply(sumstat.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list <- sapply(sumstat.files, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list <- lapply(sumstat.list, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -114,10 +111,7 @@ MetaSTAAR_merge_varlist <- function(chr,variant_pos,study.names,sample.sizes,sum
 
     ### covariance matrices
     cov.files <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    cov.list <- lapply(cov.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list <- sapply(cov.files, function(x) mget(load(x)), simplify = TRUE)
     cov.list <- lapply(cov.list, function(x) {
       if (is.null(x)) {
         as(matrix(nrow=0,ncol=0),"dgCMatrix")
@@ -148,10 +142,7 @@ MetaSTAAR_merge_varlist <- function(chr,variant_pos,study.names,sample.sizes,sum
   }else if (max(variant_pos) <= (segment + 1) * segment.size) {
     ### summary statistics
     sumstat.files1 <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list1 <- lapply(sumstat.files1, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list1 <- sapply(sumstat.files1, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list1 <- lapply(sumstat.list1, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -170,10 +161,7 @@ MetaSTAAR_merge_varlist <- function(chr,variant_pos,study.names,sample.sizes,sum
     }, x = sumstat.list1, y = cov_maf_cutoff, SIMPLIFY = FALSE)
 
     sumstat.files2 <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment+1,".Rdata")
-    sumstat.list2 <- lapply(sumstat.files2, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list2 <- sapply(sumstat.files2, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list2 <- lapply(sumstat.list2, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -248,10 +236,7 @@ MetaSTAAR_merge_varlist <- function(chr,variant_pos,study.names,sample.sizes,sum
 
     ### covariance matrices
     cov.files1 <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    cov.list1 <- lapply(cov.files1, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list1 <- sapply(cov.files1, function(x) mget(load(x)), simplify = TRUE)
     cov.list1 <- mapply(function(x,y,z) {
       if (is.null(x)) {
         x <- as(matrix(nrow=length(y),ncol=(length(y)+length(z))),"dgCMatrix")
@@ -260,10 +245,7 @@ MetaSTAAR_merge_varlist <- function(chr,variant_pos,study.names,sample.sizes,sum
     }, x = cov.list1, y = position.index1, z = position.index2, SIMPLIFY = FALSE)
 
     cov.files2 <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment+1,".Rdata")
-    cov.list2 <- lapply(cov.files2, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list2 <- sapply(cov.files2, function(x) mget(load(x)), simplify = TRUE)
     cov.list2 <- lapply(cov.list2, function(x) {
       if (is.null(x)) {
         as(matrix(nrow=0,ncol=0),"dgCMatrix")

R/MetaSTAAR_merge_varlist_cond.R

@@ -67,10 +67,7 @@ MetaSTAAR_merge_varlist_cond <- function(chr,variant_pos,study.names,sample.size
   if (max(variant_pos) <= segment * segment.size) {
     ### summary statistics
     sumstat.files <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list <- lapply(sumstat.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list <- sapply(sumstat.files, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list <- lapply(sumstat.list, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -126,10 +123,7 @@ MetaSTAAR_merge_varlist_cond <- function(chr,variant_pos,study.names,sample.size
 
     ### covariance matrices
     cov.files <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    cov.list <- lapply(cov.files, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list <- sapply(cov.files, function(x) mget(load(x)), simplify = TRUE)
     cov.list <- lapply(cov.list, function(x) {
       if (is.null(x)) {
         as(matrix(nrow=0,ncol=0),"dgCMatrix")
@@ -160,10 +154,7 @@ MetaSTAAR_merge_varlist_cond <- function(chr,variant_pos,study.names,sample.size
   }else if (max(variant_pos) <= (segment + 1) * segment.size) {
     ### summary statistics
     sumstat.files1 <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    sumstat.list1 <- lapply(sumstat.files1, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list1 <- sapply(sumstat.files1, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list1 <- lapply(sumstat.list1, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -182,10 +173,7 @@ MetaSTAAR_merge_varlist_cond <- function(chr,variant_pos,study.names,sample.size
     }, x = sumstat.list1, y = cov_maf_cutoff, SIMPLIFY = FALSE)
 
     sumstat.files2 <- paste0(sumstat.dir,"/summary.stat.",trait,".",study.names,".chr",chr,".segment",segment+1,".Rdata")
-    sumstat.list2 <- lapply(sumstat.files2, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "summary.stat"])
-    })
+    sumstat.list2 <- sapply(sumstat.files2, function(x) mget(load(x)), simplify = TRUE)
     sumstat.list2 <- lapply(sumstat.list2, function(x) {
       if (!(is.null(x)) && !("qc_label" %in% colnames(x))){
         data.frame(x[,1:4],qc_label="PASS",x[,5:dim(x)[2]],stringsAsFactors = FALSE)
@@ -260,10 +248,7 @@ MetaSTAAR_merge_varlist_cond <- function(chr,variant_pos,study.names,sample.size
 
     ### covariance matrices
     cov.files1 <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment,".Rdata")
-    cov.list1 <- lapply(cov.files1, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list1 <- sapply(cov.files1, function(x) mget(load(x)), simplify = TRUE)
     cov.list1 <- mapply(function(x,y,z) {
       if (is.null(x)) {
         x <- as(matrix(nrow=length(y),ncol=(length(y)+length(z))),"dgCMatrix")
@@ -272,10 +257,7 @@ MetaSTAAR_merge_varlist_cond <- function(chr,variant_pos,study.names,sample.size
     }, x = cov.list1, y = position.index1, z = position.index2, SIMPLIFY = FALSE)
 
     cov.files2 <- paste0(cov.dir,"/GTSinvG.rare.",trait,".",study.names,".chr",chr,".segment",segment+1,".Rdata")
-    cov.list2 <- lapply(cov.files2, function(x) {
-      load(file = x)
-      get(ls()[ls()!= "cov"])
-    })
+    cov.list2 <- sapply(cov.files2, function(x) mget(load(x)), simplify = TRUE)
     cov.list2 <- lapply(cov.list2, function(x) {
       if (is.null(x)) {
         as(matrix(nrow=0,ncol=0),"dgCMatrix")
@@ -371,10 +353,7 @@ MetaSTAAR_merge_varlist_cond <- function(chr,variant_pos,study.names,sample.size
 
   ### covariance files for conditional analysis
   covcond.files <- paste0(covcond.dir,"/cov.cond.",trait,".",study.names,".chr",chr,".region.",region,".Rdata")
-  covcond.list <- lapply(covcond.files, function(x) {
-    load(file = x)
-    get(ls()[ls()!= "cov.cond"])
-  })
+  covcond.list <- sapply(covcond.files, function(x) mget(load(x)), simplify = TRUE)
   variant_info_list <- lapply(covcond.list, function(x) {x$variant_info})
   variant_info_merge <- do.call("rbind",variant_info_list)
   variant_info_nodup <- variant_info_merge[!duplicated(variant_info_merge),]

R/MetaSTAAR_worker_cov.R

@@ -35,7 +35,7 @@
 MetaSTAAR_worker_cov <- function(genotype,obj_nullmodel,cov_maf_cutoff,
                                  variant_pos,region_midpos,qc_label=NULL,segment.size=5e5,signif.digits=3){
 
-  if(!inherits(genotype, "matrix") && !inherits(genotype, "sparseMatrix")){
+  if(!inherits(genotype, "matrix") && !inherits(genotype, "Matrix")){
     stop("genotype is not a matrix!")
   }
 

R/MetaSTAAR_worker_cov_cond.R

@@ -39,7 +39,7 @@
 
 MetaSTAAR_worker_cov_cond <- function(genotype,genotype_adj,obj_nullmodel,variant_info,variant_adj_info){
 
-  if(!inherits(genotype, "matrix") && !inherits(genotype, "sparseMatrix")){
+  if(!inherits(genotype, "matrix") && !inherits(genotype, "Matrix")){
     stop("genotype is not a matrix!")
   }
 

R/MetaSTAAR_worker_sumstat.R

@@ -26,7 +26,7 @@
 
 MetaSTAAR_worker_sumstat <- function(genotype,obj_nullmodel,variant_info,qc_label=NULL){
 
-  if(!inherits(genotype, "matrix") && !inherits(genotype, "sparseMatrix")){
+  if(!inherits(genotype, "matrix") && !inherits(genotype, "Matrix")){
     stop("genotype is not a matrix!")
   }