Merge pull request #15 from large-scale-gxe-methods/dev

Dev

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MAGEE
-Version: 1.3.1
-Date: 2023-10-12
+Version: 1.3.2
+Date: 2023-11-17
 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]"),

R/MAGEE.meta.R

@@ -149,7 +149,7 @@ MAGEE.meta <- function(meta.files.prefix, n.files = rep(1, length(meta.files.pre
           IDX3 <- IDX3+n.p*n.E*(cohort.group.idx[j]-1)
         }
         U[IDX] <- U[IDX]+U.list[[j]]$G.SCORE[IDX2]
-        SK[IDX3] <- SK[IDX3]+as.vector(U.list[[j]][, paste("K.SCORE.", 1:n.E, sep="")])[IDX4]
+        SK[IDX3] <- SK[IDX3]+as.vector(as.matrix(U.list[[j]][, paste("K.SCORE.", 1:n.E, sep="")]))[IDX4]
         V[IDX, IDX] <- V[IDX,IDX]+V.list[[j]][IDX2,IDX2]
         KPG[IDX3,IDX] <- KPG[IDX3,IDX]+KPG.list[[j]][IDX4,IDX2]
         KPK[IDX3,IDX3] <- KPK[IDX3,IDX3]+KPK.list[[j]][IDX4,IDX4]

inst/doc/MAGEE.Rnw

@@ -7,7 +7,7 @@
 \usepackage{graphicx}
 \usepackage{epstopdf}
 \usepackage{hyperref}
-\usepackage[usenames,dvipsnames]{xcolor}
+\usepackage[dvipsnames]{xcolor}
 \usepackage{listings}
 \usepackage[superscript]{cite}
 \newcommand{\mb}{\mathbf}
@@ -38,8 +38,8 @@ morekeywords={}
 
 \begin{document}
 \SweaveOpts{concordance=TRUE}
-\title{MAGEE: Mixed Model Association Test for GEne-Environment Interaction\\Version 1.3.1}
-\date{October 12, 2023}
+\title{MAGEE: Mixed Model Association Test for GEne-Environment Interaction\\Version 1.3.2}
+\date{November 17, 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
@@ -479,6 +479,12 @@ Initial public release of \textit{MAGEE}.
 \item Bioconductor packages \textbf{SeqArray} and \textbf{SeqVarTools} moved to Suggests.
 \end{enumerate}
 
+\subsection{Version 1.3.2 (November 17, 2023)}
+\begin{enumerate}
+\item Fixed a minor bug in \textbf{MAGEE.meta} when meta-analyzing interactions with multiple exposures.
+\item Removed the "usernames" option for xcolor.sty.
+\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 1.3.1\cr
-Date: \tab 2023-10-12\cr
+Version: \tab 1.3.2\cr
+Date: \tab 2023-11-17\cr
 License: \tab GPL (>= 3)\cr
 }
 }

vignettes/MAGEE.Rnw

@@ -7,7 +7,7 @@
 \usepackage{graphicx}
 \usepackage{epstopdf}
 \usepackage{hyperref}
-\usepackage[usenames,dvipsnames]{xcolor}
+\usepackage[dvipsnames]{xcolor}
 \usepackage{listings}
 \usepackage[superscript]{cite}
 \newcommand{\mb}{\mathbf}
@@ -38,9 +38,9 @@ morekeywords={}
 
 \begin{document}
 \SweaveOpts{concordance=TRUE}
-\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]} 
+\title{MAGEE: Mixed Model Association Test for GEne-Environment Interaction\\Version 1.3.2}
+\date{November 17, 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\\Department of Epidemiology\\School of Public Health\\The University of Texas Health Science Center at Houston\\Email: [email protected]\\\\Duy Pham\\Human Genetics Center\\Department of Epidemiology\\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\\Department of Epidemiology\\School of Public Health\\The University of Texas Health Science Center at Houston\\Email: [email protected]} 
 
 \maketitle
 \newpage
@@ -479,6 +479,12 @@ Initial public release of \textit{MAGEE}.
 \item Bioconductor packages \textbf{SeqArray} and \textbf{SeqVarTools} moved to Suggests.
 \end{enumerate}
 
+\subsection{Version 1.3.2 (November 17, 2023)}
+\begin{enumerate}
+\item Fixed a minor bug in \textbf{MAGEE.meta} when meta-analyzing interactions with multiple exposures (thanks to: Christopher Bryan).
+\item Removed the "usernames" option for xcolor.sty.
+\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.