diff --git a/DESCRIPTION b/DESCRIPTION index af41044..44617c3 100644 --- a/DESCRIPTION +++ b/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 = "xinyu.wang@uth.tmc.edu"), person("Han", "Chen", role = c("aut", "cre"), email = "han.chen.2@uth.tmc.edu"), diff --git a/R/MAGEE.meta.R b/R/MAGEE.meta.R index 7d83666..fc4af9c 100644 --- a/R/MAGEE.meta.R +++ b/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] diff --git a/build/vignette.rds b/build/vignette.rds index 9d6dc35..9fe2680 100644 Binary files a/build/vignette.rds and b/build/vignette.rds differ diff --git a/data/example.rda b/data/example.rda index d788a0c..fd68915 100644 Binary files a/data/example.rda and b/data/example.rda differ diff --git a/inst/doc/MAGEE.Rnw b/inst/doc/MAGEE.Rnw index 0a0e5c6..2ba33b2 100644 --- a/inst/doc/MAGEE.Rnw +++ b/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: Xinyu.Wang@uth.tmc.edu\\\\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: Han.Chen.2@uth.tmc.edu\\\\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: duy.t.pham@uth.tmc.edu\\\\Kenneth Westerman\\Department of Medicine\\Clinical and Translational Epidemiology Unit\\Mongan Institute\\Massachusetts General Hospital\\Email: KEWESTERMAN@mgh.harvard.edu\\\\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: cong.pan@uth.tmc.edu} \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 (Han.Chen.2@uth.tmc.edu). For bug reports, please include an example to reproduce the problem without having to access your confidential data. diff --git a/inst/doc/MAGEE.pdf b/inst/doc/MAGEE.pdf index 601e74b..5d7f04f 100644 Binary files a/inst/doc/MAGEE.pdf and b/inst/doc/MAGEE.pdf differ diff --git a/man/MAGEE-package.Rd b/man/MAGEE-package.Rd index ecc4249..7a866a5 100644 --- a/man/MAGEE-package.Rd +++ b/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 } } diff --git a/vignettes/MAGEE.Rnw b/vignettes/MAGEE.Rnw index 0a0e5c6..2fccb23 100644 --- a/vignettes/MAGEE.Rnw +++ b/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: Xinyu.Wang@uth.tmc.edu\\\\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: Han.Chen.2@uth.tmc.edu\\\\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: duy.t.pham@uth.tmc.edu\\\\Kenneth Westerman\\Department of Medicine\\Clinical and Translational Epidemiology Unit\\Mongan Institute\\Massachusetts General Hospital\\Email: KEWESTERMAN@mgh.harvard.edu\\\\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: cong.pan@uth.tmc.edu} +\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: Xinyu.Wang@uth.tmc.edu\\\\Han Chen\\Human Genetics Center\\Department of Epidemiology\\School of Public Health\\The University of Texas Health Science Center at Houston\\Email: Han.Chen.2@uth.tmc.edu\\\\Duy Pham\\Human Genetics Center\\Department of Epidemiology\\School of Public Health\\The University of Texas Health Science Center at Houston\\Email: duy.t.pham@uth.tmc.edu\\\\Kenneth Westerman\\Department of Medicine\\Clinical and Translational Epidemiology Unit\\Mongan Institute\\Massachusetts General Hospital\\Email: KEWESTERMAN@mgh.harvard.edu\\\\Cong Pan\\Human Genetics Center\\Department of Epidemiology\\School of Public Health\\The University of Texas Health Science Center at Houston\\Email: cong.pan@uth.tmc.edu} \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 (Han.Chen.2@uth.tmc.edu). For bug reports, please include an example to reproduce the problem without having to access your confidential data.