From be3622daad3c099a532806f1ed839f5480462461 Mon Sep 17 00:00:00 2001 From: Julian Stamp Date: Thu, 1 Dec 2022 10:54:48 -0500 Subject: [PATCH] MM-89: place holder for biorxiv (#92) * MM-89: place holder for biorxiv * MM-89: place biorXiv citation --- DESCRIPTION | 4 +++- NEWS.md | 9 ++++++++- README.md | 7 ++++--- vignettes/mvMAPIT.Rmd | 23 +++++++++++++++++------ 4 files changed, 32 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cfa82845..8f407f9f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -22,7 +22,9 @@ Description: Epistasis, commonly defined as the interaction between genetic loci structures between traits to improve the identification of variants involved in epistasis. We formulate mvMAPIT as a multivariate linear mixed model and develop a multi-trait variance component estimation algorithm for efficient parameter inference and P-value computation. Together with reasonable model approximations, our proposed approach is - scalable to moderately sized GWA studies. Crawford et al. (2017) . + scalable to moderately sized GWA studies. + Crawford et al. (2017) . + Stamp et al. (2022) . License: GPL (>= 3) Depends: R (>= 3.5) diff --git a/NEWS.md b/NEWS.md index 5aaa7a7d..46189924 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,16 @@ # mvMAPIT (development version) +# mvMAPIT 2.0.0 release + +* `fishers_combined` and `harmonic_combined` now take additional arguments in +form of string values. The first determines the name of the column of the tibble +by which to group the p-values. The second determines the name of the column + containing the p-values. * Added `Dockerfile` and vignette on mvMAPIT in Docker. * `MvMAPIT` was renamed to `mvmapit`. * `simulate_phenotypes` was renamed to `simulate_traits`. -* Dependencies were cleaned up, e.g. R requirement 2.10 -> 3.5, old package dependencies removed. +* Dependencies were cleaned up, e.g. R requirement 2.10 -> 3.5, old package +dependencies removed. # mvMAPIT 1.1.1-alpha prerelease * Version that publication data was produced with. No official release. diff --git a/README.md b/README.md index e1ce3fd8..a050a788 100644 --- a/README.md +++ b/README.md @@ -167,15 +167,16 @@ For questions or concerns with the MAPIT functions, please contact We appreciate any feedback you may have with our repository and instructions. - - ## References [^1]: L. Crawford, P. Zeng, S. Mukherjee, X. Zhou (2017). Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits. *PLoS Genet*. **13**(7): e1006869. -[^2]: J. Stamp, A. DenAdel, D. Weinreich, L. Crawford (2022). Multivariate MAPIT. +[^2]: J. Stamp, A. DenAdel, D. Weinreich, L. Crawford (2022). Leveraging the + Genetic Correlation between Traits Improves the Detection of Epistasis in + Genome-wide Association Studies. bioRxiv 2022.11.30.518547; doi: + [^3]: X. Zhou (2017). A unified framework for variance component estimation with summary statistics in genome-wide association studies. *Ann Appl Stat*. **11**(4): 2027-2051. diff --git a/vignettes/mvMAPIT.Rmd b/vignettes/mvMAPIT.Rmd index 07f5d8e2..788e8cab 100644 --- a/vignettes/mvMAPIT.Rmd +++ b/vignettes/mvMAPIT.Rmd @@ -21,12 +21,23 @@ knitr::opts_chunk$set( library(knitr) ``` -**_NOTE:_** if you use mvMAPIT in published research, please cite: - -* Crawford, L., Zeng, P., Mukherjee, S., & Zhou, X. (2017). Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits. PLoS genetics, 13(7), e1006869. -* Stamp, J., DenAdel, A., Weinreich, D. & Crawford, L. (2022). Multivariate MAPIT. -* Stamp J, Crawford L (2022). mvMAPIT: Multivariate Genome Wide Marginal Epistasis Test. https://github.com/lcrawlab/mvMAPIT, https://lcrawlab.github.io/mvMAPIT/ - +### Please Cite Us + +If you use mvMAPIT in published research, please cite: + +> * Crawford L, Zeng P, Mukherjee S, & Zhou X (2017). Detecting epistasis +> with the marginal epistasis test in genetic mapping studies of quantitative +> traits. PLoS genetics, 13(7), e1006869. +> +> +> * Stamp J, DenAdel A, Weinreich D, Crawford, L (2022). Leveraging the +> Genetic Correlation between Traits Improves the Detection of Epistasis in +> Genome-wide Association Studies. bioRxiv 2022.11.30.518547; doi: +> +> +> * Stamp J, Crawford L (2022). mvMAPIT: Multivariate Genome Wide Marginal +> Epistasis Test. , +> # Getting Started Load necessary libraries. For the sake of getting started, `mvMAPIT` comes with