MM-89: place holder for biorxiv (#92)

* MM-89: place holder for biorxiv

* MM-89: place biorXiv citation

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) <doi:10.1371/journal.pgen.1006869>.
+  scalable to moderately sized GWA studies.
+  Crawford et al. (2017) <doi:10.1371/journal.pgen.1006869>.
+  Stamp et al. (2022) <doi:10.1101/2022.11.30.518547>.
 License: GPL (>= 3)
 Depends:
     R (>= 3.5)

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.

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.
     <https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006869>
 
-[^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:
+    <https://doi.org/10.1101/2022.11.30.518547>
 
 [^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.

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.
+>   <https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006869>
+>
+> * 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:
+>    <https://doi.org/10.1101/2022.11.30.518547>
+>
+> * Stamp J, Crawford L (2022). mvMAPIT: Multivariate Genome Wide Marginal
+>   Epistasis Test. <https://github.com/lcrawlab/mvMAPIT>,
+>   <https://lcrawlab.github.io/mvMAPIT/>
 
 # Getting Started
 Load necessary libraries. For the sake of getting started, `mvMAPIT` comes with