Merge pull request #13 from large-scale-gxe-methods/dev

v1.3.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MAGEE
-Version: 1.3.0
-Date: 2023-04-18
+Version: 1.3.1
+Date: 2023-10-12
 Title: Mixed Model Association Test for GEne-Environment Interaction
 Authors@R: c(person("Xinyu", "Wang", role = "aut", email = "[email protected]"),
              person("Han", "Chen", role = c("aut", "cre"), email = "[email protected]"),
@@ -13,9 +13,9 @@ Authors@R: c(person("Xinyu", "Wang", role = "aut", email = "[email protected]
 Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
 License: GPL (>= 3)
 Copyright: See COPYRIGHTS for details.
-Imports: Rcpp, Matrix, parallel, MASS, SeqArray, SeqVarTools, foreach,
-        GMMAT, CompQuadForm, data.table
-Suggests: doMC, testthat
+Imports: Rcpp, Matrix, parallel, MASS, foreach, GMMAT, CompQuadForm,
+        data.table
+Suggests: doMC, SeqArray, SeqVarTools, testthat
 LinkingTo: Rcpp, RcppArmadillo
 Encoding: UTF-8
 Depends: R (>= 3.2.0)

NAMESPACE

@@ -8,8 +8,6 @@ importFrom("stats", "as.formula", "binomial", "dbeta", "glm", "model.frame",
 importFrom("utils", "read.table", "write.table")
 importFrom("CompQuadForm", "davies", "liu")
 importFrom("data.table", "fread")
-importFrom("SeqArray", "seqOpen", "seqGetData", "seqClose", "seqSetFilter")
-importFrom("SeqVarTools", "missingGenotypeRate", "alleleFrequency", "altDosage")
 importFrom("GMMAT", "glmmkin", "glmm.score", "SMMAT")
 useDynLib(MAGEE, .registration = TRUE, .fixes = "C_")
 export(MAGEE, glmm.gei,  MAGEE.prep, MAGEE.lowmem, MAGEE.meta, glmm.gei.meta)

README.md

@@ -12,7 +12,7 @@ See Section 3.2 of the <a href="https://github.com/large-scale-gxe-methods/MAGEE
 For optimal computational performance, it is recommended to use an R version configured with the Intel Math Kernel Library (or other fast BLAS/LAPACK libraries). See the <a href="https://www.intel.com/content/www/us/en/developer/articles/technical/using-onemkl-with-r.html">instructions</a> on building R with Intel MKL.
 
 ## Version
-The current version is 1.3.0 (April 18, 2023).
+The current version is 1.3.1 (October 12, 2023).
 
 ## License
 This software is licensed under GPL (>= 3).
@@ -25,5 +25,6 @@ This work was supported by National Institutes of Health (NIH) grants R00 HL1305
 
 ## References
 <p>Please cite
-<li>Wang X, Lim E, Liu C, Sung YJ, Rao DC, Morrison AC, Boerwinkle E, Manning AK, Chen H. (2020) Efficient gene-environment interaction tests for large biobank-scale sequencing studies. <em>Genetic Epidemiology</em> <b>44(8):</b> 908-923. DOI: <a href="https://doi.org/10.1002/gepi.22351">10.1002/gepi.22351</a>.</li></p>
-
+<li>Wang X, Lim E, Liu C, Sung YJ, Rao DC, Morrison AC, Boerwinkle E, Manning AK, Chen H. (2020) Efficient gene-environment interaction tests for large biobank-scale sequencing studies. <em>Genetic Epidemiology</em> <b>44(8):</b> 908-923. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32864785">32864785</a>. PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7754763/">PMC7754763</a>. DOI: <a href="https://doi.org/10.1002/gepi.22351">10.1002/gepi.22351</a>.</li></p>
+<p>If you use MAGEE meta-analysis, please also cite
+<li>Wang X, Pham DT, Westerman KE, Pan C, Manning AK, Chen H. (2022) Genomic summary statistics and meta-analysis for set-based gene-environment interaction tests in large-scale sequencing studies. <em>medRxiv</em> 2022.05.08.22274819. DOI: <a href="https://doi.org/10.1101/2022.05.08.22274819">https://doi.org/10.1101/2022.05.08.22274819</a>.</li></p>

inst/doc/MAGEE.R

@@ -63,7 +63,6 @@
 ###################################################
 ### code chunk number 8: MAGEEgeigds (eval = FALSE)
 ###################################################
-## outfile <- tempfile()
 ## infile1 <- system.file("extdata", "meta1.txt", package = "MAGEE")
 ## infile2 <- system.file("extdata", "meta2.txt", package = "MAGEE")
 ## infile3 <- system.file("extdata", "meta3.txt", package = "MAGEE")

inst/doc/MAGEE.Rnw

@@ -38,8 +38,8 @@ morekeywords={}
 
 \begin{document}
 \SweaveOpts{concordance=TRUE}
-\title{MAGEE: Mixed Model Association Test for GEne-Environment Interaction\\Version 1.3.0}
-\date{April 18, 2023}
+\title{MAGEE: Mixed Model Association Test for GEne-Environment Interaction\\Version 1.3.1}
+\date{October 12, 2023}
 \author{Xinyu Wang\\Human Genetics Center\\Dept. of Biostatistics and Data Science\\School of Public Health\\The University of Texas Health Science Center at Houston\\Email: [email protected]\\\\Han Chen\\Human Genetics Center\\Dept. of Epidemiology, Human Genetics and Environmental Sciences\\School of Public Health\\Center for Precision Health\\School of Biomedical Informatics\\The University of Texas Health Science Center at Houston\\Email: [email protected]\\\\Duy Pham\\Human Genetics Center\\Dept. of Epidemiology, Human Genetics and Environmental Sciences\\School of Public Health\\The University of Texas Health Science Center at Houston\\Email: [email protected]\\\\Kenneth Westerman\\Department of Medicine\\Clinical and Translational Epidemiology Unit\\Mongan Institute\\Massachusetts General Hospital\\Email: [email protected]\\\\Cong Pan\\Human Genetics Center\\Dept. of Epidemiology, Human Genetics and Environmental Sciences\\School of Public Health\\The University of Texas Health Science Center at Houston\\Email: [email protected]} 
 
 \maketitle
@@ -82,7 +82,7 @@ Note: The main effect variance component test (MV) in \textit{MAGEE} is the same
 \textit{MAGEE} is an open source project and is freely available for download at \url{https://github.com/xwang21/MAGEE}. It can also be found as a regular R package and downloaded from CRAN (\url{https://CRAN.R-project.org/package=MAGEE}).
 
 \subsection{Installing \textit{MAGEE}}
-The following R packages are required before installing \textit{MAGEE}: \href{https://cran.r-project.org/web/packages/Rcpp/index.html}{Rcpp} and \href{https://cran.r-project.org/web/packages/RcppArmadillo/index.html}{RcppArmadillo} for R and C++ integration and \href{https://cran.r-project.org/web/packages/testthat/index.html}{testthat} to run code checks during development. Additionally, \textit{MAGEE} imports from \href{https://cran.r-project.org/web/packages/Rcpp/index.html}{Rcpp}, \href{https://cran.r-project.org/web/packages/CompQuadForm/index.html}{CompQuadForm}, \href{https://cran.r-project.org/web/packages/foreach/index.html}{foreach}, \href{https://cran.r-project.org/web/views/HighPerformanceComputing.html}{parallel}, \href{https://cran.r-project.org/web/packages/Matrix/index.html}{Matrix}, methods, \href{https://cran.r-project.org/web/packages/GMMAT/index.html}{GMMAT}, \href{https://cran.r-project.org/web/packages/data.table/index.html}{data.table}, and Bioconductor packages \href{http://bioconductor.org/packages/release/bioc/html/SeqArray.html}{SeqArray} and \href{http://bioconductor.org/packages/release/bioc/html/SeqVarTools.html}{SeqVarTools}. The R package \href{https://cran.r-project.org/web/packages/doMC/index.html}{doMC} is required to run parallel computing in \textbf{glmm.gei} and \textbf{MAGEE} (\href{https://cran.r-project.org/web/packages/doMC/index.html}{doMC} is not available on Windows and these functions will switch to a single compute thread). 
+\textit{MAGEE} links to R packages \href{https://cran.r-project.org/web/packages/Rcpp/index.html}{Rcpp} and \href{https://cran.r-project.org/web/packages/RcppArmadillo/index.html}{RcppArmadillo}, and also imports R packages \href{https://cran.r-project.org/web/packages/Rcpp/index.html}{Rcpp}, \href{https://cran.r-project.org/web/packages/CompQuadForm/index.html}{CompQuadForm}, \href{https://cran.r-project.org/web/packages/foreach/index.html}{foreach}, \href{https://cran.r-project.org/web/views/HighPerformanceComputing.html}{parallel}, \href{https://cran.r-project.org/web/packages/Matrix/index.html}{Matrix}, methods, \href{https://cran.r-project.org/web/packages/GMMAT/index.html}{GMMAT}, \href{https://cran.r-project.org/web/packages/data.table/index.html}{data.table}. \textit{MAGEE} requires Bioconductor packages \href{http://bioconductor.org/packages/release/bioc/html/SeqArray.html}{SeqArray} and \href{http://bioconductor.org/packages/release/bioc/html/SeqVarTools.html}{SeqVarTools} to work with genotype files in the GDS format. In addition, \textit{GMMAT} requires \href{https://cran.r-project.org/web/packages/testthat/index.html}{testthat} to run code checks during development, and \href{https://cran.r-project.org/web/packages/doMC/index.html}{doMC} to run parallel computing in \textbf{glmm.gei} and \textbf{MAGEE} for genotype files in the GDS format (however, \href{https://cran.r-project.org/web/packages/doMC/index.html}{doMC} is not available on Windows and these functions will switch to a single thread). These dependencies should be installed before installing \textit{MAGEE}.
 
 For optimal computational performance, it is recommended to use an R version configured with the Intel Math Kernel Library (or other fast BLAS/LAPACK libraries). See the instructions on building R with Intel MKL (\url{https://software.intel.com/en-us/articles/using-intel-mkl-with-r}).
 
@@ -168,7 +168,6 @@ glmm.gei(model0, interaction='sex', geno.file = infile,
 The function \textbf{glmm.gei} returns no value for GDS and BGEN genotype files.
 \subsubsection{meta-analysis}
 <<MAGEEgeigds, eval=FALSE, echo=TRUE>>=
-outfile <- tempfile()
 infile1 <- system.file("extdata", "meta1.txt", package = "MAGEE")
 infile2 <- system.file("extdata", "meta2.txt", package = "MAGEE")
 infile3 <- system.file("extdata", "meta3.txt", package = "MAGEE")
@@ -475,6 +474,11 @@ Initial public release of \textit{MAGEE}.
 \item Minor changes in the man directory, per CRAN policy.
 \end{enumerate}
 
+\subsection{Version 1.3.1 (October 12, 2023)}
+\begin{enumerate}
+\item Bioconductor packages \textbf{SeqArray} and \textbf{SeqVarTools} moved to Suggests.
+\end{enumerate}
+
 \section{Contact}
 Please refer to the R help document of \textit{MAGEE} for specific questions about each function. For comments, suggestions, bug reports and questions, please contact Han Chen ([email protected]). For bug reports, please include an example to reproduce the problem without having to access your confidential data.
 

man/MAGEE-package.Rd

@@ -11,8 +11,8 @@ An R package for performing generalized linear mixed model-based single-variant
 \tabular{ll}{
 Package: \tab MAGEE\cr
 Type: \tab Package\cr
-Version: \tab 1.3.0\cr
-Date: \tab 2023-04-18\cr
+Version: \tab 1.3.1\cr
+Date: \tab 2023-10-12\cr
 License: \tab GPL (>= 3)\cr
 }
 }

man/MAGEE.Rd

@@ -155,16 +155,19 @@ Xinyu Wang, Han Chen, Duy Pham
 }
 \examples{
 \donttest{
-library(GMMAT)
-    data(example)
-    attach(example)
-    model0 <- glmmkin(disease ~ age + sex, data = pheno, kins = GRM,
+if(requireNamespace("SeqArray", quietly = TRUE) && requireNamespace("SeqVarTools",
+  quietly = TRUE)) {
+  library(GMMAT)
+  data(example)
+  attach(example)
+  model0 <- glmmkin(disease ~ age + sex, data = pheno, kins = GRM,
     id = "id", family = binomial(link = "logit"))
-    geno.file <- system.file("extdata", "geno.gds", package = "MAGEE")
-    group.file <- system.file("extdata", "SetID.withweights.txt", package = "MAGEE")
-    out <- MAGEE(model0, interaction='sex', geno.file, group.file, group.file.sep = "\t",
-                 tests=c("JV", "JF", "JD"))
-    print(out)
+  geno.file <- system.file("extdata", "geno.gds", package = "MAGEE")
+  group.file <- system.file("extdata", "SetID.withweights.txt", package = "MAGEE")
+  out <- MAGEE(model0, interaction='sex', geno.file, group.file, group.file.sep = "\t",
+    tests=c("JV", "JF", "JD"))
+  print(out)
+}
 }
 }
 \keyword{ variant set-based test }

man/MAGEE.meta.Rd

@@ -95,7 +95,9 @@ Xinyu Wang, Han Chen, Duy Pham
 }
 \examples{
 \donttest{
-library(GMMAT)
+if(requireNamespace("SeqArray", quietly = TRUE) && requireNamespace("SeqVarTools",
+  quietly = TRUE)) {
+  library(GMMAT)
   data(example)
   attach(example)
   model0 <- glmmkin(disease ~ age + sex, data = pheno, kins = GRM,
@@ -110,7 +112,8 @@ library(GMMAT)
   print(out)
   out1 <- MAGEE.meta(meta.file.prefix, group.file = group.file, tests = c("JV","JF","JD"))
   print(out1)
-  unlink(paste0(meta.file.prefix, c("score", "cov"), ".1"))
+  unlink(paste0(meta.file.prefix, c(".score", ".cov"), ".1"))
+}
 }
 }
 \keyword{ variant set-based test }

man/glmm.gei.Rd

@@ -73,17 +73,19 @@ Xinyu Wang, Han Chen, Duy Pham
   model0 <- glmmkin(disease ~ age + sex, data = pheno, kins = GRM,
                     id = "id", family = binomial(link = "logit"))
                    
-  infile <- system.file("extdata", "geno.gds", package = "MAGEE")
-  gds_outfile <- tempfile()
-  glmm.gei(model0, interaction='sex', geno.file = infile, outfile = gds_outfile)
-  
+  if(requireNamespace("SeqArray", quietly = TRUE) && requireNamespace("SeqVarTools",
+    quietly = TRUE)) {
+    infile <- system.file("extdata", "geno.gds", package = "MAGEE")
+    gds_outfile <- tempfile()
+    glmm.gei(model0, interaction='sex', geno.file = infile, outfile = gds_outfile)
+    unlink(gds_outfile)
+  }
   infile <- system.file("extdata", "geno.bgen", package = "MAGEE")
   samplefile <- system.file("extdata", "geno.sample", package = "MAGEE")
   bgen_outfile <- tempfile()
   glmm.gei(model0, interaction='sex', geno.file = infile, outfile = bgen_outfile,
            bgen.samplefile = samplefile)
-  
-  unlink(c(bgen_outfile, gds_outfile))
+  unlink(bgen_outfile)
 }
 \keyword{ generalized linear mixed model }
 \keyword{ gene-environment interaction }

tests/testthat/test_MAGEE.R

@@ -1,5 +1,6 @@
 test_that("cross-sectional gaussian", {
-
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   bgenfile <- system.file("extdata", "geno.bgen", package = "MAGEE")
   samplefile <- system.file("extdata", "geno.sample", package = "MAGEE")
@@ -115,7 +116,8 @@ test_that("cross-sectional gaussian", {
 
 test_that("cross-sectional binomial", {
   skip_on_cran()
-
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile <- system.file("extdata", "geno.gds", package = "MAGEE")
   bgenfile <- system.file("extdata", "geno.bgen", package = "MAGEE")
   samplefile <- system.file("extdata", "geno.sample", package = "MAGEE")
@@ -231,7 +233,8 @@ test_that("cross-sectional binomial", {
 ### multi-phenotype MAGEE
 test_that("multiple phenotypes gaussian", {
   skip_on_cran()
-
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile <- system.file("extdata", "geno.gds", package = "MAGEE")
   bgenfile <- system.file("extdata", "geno.bgen", package = "MAGEE")
   samplefile <- system.file("extdata", "geno.sample", package = "MAGEE")
@@ -348,7 +351,8 @@ test_that("multiple phenotypes gaussian", {
 ### longitudinal MAGEE
 test_that("longitudinal random time trend gaussian", {
   skip_on_cran()
-
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   bgenfile <- system.file("extdata", "geno.bgen", package = "MAGEE")
   samplefile <- system.file("extdata", "geno.sample", package = "MAGEE")

tests/testthat/test_MAGEE.meta.R

@@ -1,4 +1,6 @@
 test_that("cross-sectional id le 400 binomial", {
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   group.file <- system.file("extdata", "SetID.withweights.txt", package = "MAGEE")
   data(example)
@@ -40,6 +42,8 @@ test_that("cross-sectional id le 400 binomial", {
 
 test_that("cross-sectional id gt 400 binomial", {
   skip_on_cran()
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   group.file <- system.file("extdata", "SetID.withweights.txt", package = "MAGEE")
   data(example)
@@ -70,6 +74,8 @@ test_that("cross-sectional id gt 400 binomial", {
 
 test_that("cross-sectional id le 400 gaussian", {
   skip_on_cran()
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   group.file <- system.file("extdata", "SetID.withweights.txt", package = "MAGEE")
   data(example)
@@ -98,6 +104,8 @@ test_that("cross-sectional id le 400 gaussian", {
 
 test_that("cross-sectional id gt 400 gaussian", {
   skip_on_cran()
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   group.file <- system.file("extdata", "SetID.withweights.txt", package = "MAGEE")
   data(example)
@@ -127,7 +135,8 @@ test_that("cross-sectional id gt 400 gaussian", {
 
 test_that("longitudinal repeated measures gaussian", {
   skip_on_cran()
-
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile <- system.file("extdata", "geno.gds", package = "MAGEE")
   group.file <- system.file("extdata", "SetID.withweights.txt", package = "MAGEE")
   data(example)
@@ -149,7 +158,8 @@ test_that("longitudinal repeated measures gaussian", {
 
 test_that("longitudinal random time trend gaussian", {
   skip_on_cran()
-
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile <- system.file("extdata", "geno.gds", package = "MAGEE")
   group.file <- system.file("extdata", "SetID.withweights.txt", package = "MAGEE")
   data(example)

tests/testthat/test_glmm.gei.R

@@ -1,5 +1,6 @@
 test_that("cross-sectional gaussian", {
-
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   bgenfile <- system.file("extdata", "geno.bgen", package = "MAGEE")
   samplefile <- system.file("extdata", "geno.sample", package = "MAGEE")
@@ -526,6 +527,8 @@ test_that("cross-sectional gaussian", {
 
 test_that("cross-sectional binomial", {
   skip_on_cran()
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   bgenfile <- system.file("extdata", "geno.bgen", package = "MAGEE")
   samplefile <- system.file("extdata", "geno.sample", package = "MAGEE")
@@ -1051,6 +1054,8 @@ test_that("cross-sectional binomial", {
 
 test_that("longitudinal random time trend gaussian", {
   skip_on_cran()
+  skip_if_not_installed("SeqArray")
+  skip_if_not_installed("SeqVarTools")
   gdsfile  <- system.file("extdata", "geno.gds",  package = "MAGEE")
   bgenfile <- system.file("extdata", "geno.bgen", package = "MAGEE")
   samplefile <- system.file("extdata", "geno.sample", package = "MAGEE")