README.md

In kjgleason/Primo: Package in R for Integrative Multi-Omics association analysis

Primo: Package in R for Integrative Multi-Omics association analysis

The goal of Primo is to provide computationally efficient tools to integrate data across phenotypes, cell/tissue types, populations or sources when performing joint analysis of multi-omics data.

Setup

Please note that this package uses functions from the limma package, which is downloadable from Bioconductor, and the lcmix package, which is downloadable from R-Forge. If installation of Primo fails and you have not yet installed the limma or lcmix packages, please try running the following commands:

```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("limma")

install.packages("MASS") install.packages("matrixStats") install.packages("nnls") install.packages("R.methodsS3") install.packages("lcmix",repos="http://r-forge.r-project.org") ```

Once you have installed limma and lcmix, you can install and load functions from Primo:

R devtools::install_github("kjgleason/Primo") library("Primo")

Citation

To cite Primo in publications, please use:

Kevin J. Gleason, Fan Yang, Brandon L. Pierce, Xin He, and Lin S. Chen. Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits. Genome Biol (2020); 21(1):236. doi:10.1186/s13059-020-02125-w.

Licenses

The code is released under GNU General Public License (GPL).

kjgleason/Primo documentation built on Sept. 7, 2021, 3:58 a.m.