First of all, thanks to the community for using PheGWAS. Since it’s release we have been working on a heuristic approach to give quick insights into the genetic relatedness for phenotypes using GWAS summary statistics file. We are adding this module to PheGWAS and reintroducing it as iPheGWAS (Intelligent PheGWAS). The traits in your landscape are no more ordered as random but will be ordered based on their genetic correlations.
In addition to the heuristic approach that we developed, all the functionalities outlined in the PheGWAS are also available in iphegwas package. Considering our community’s request to improve the speed of PheGWAS, the entire codebase is rewritten, and you will notice that the iphegwas package is significantly faster than the PheGWAS package.
Here is the website link to this package. Please check out the Get Started tab, and that will take you through how to use the package with automatically rendered examples. Please use chrome or firefox to generate the plots well.
Installation:
Prerequisites
Please Install plotly, devtools and Biomart before installing the iphegwas package.
Install plotly
install.packages("plotly")Install devtools
install.packages("devtools")Install BioMart
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")
