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:

  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:

  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).