carltonyfakhry/geneticsCRE: geneticsCRE is an R package that performs pathway-based genome-wide association study (PGWAS) to identify statistically significant associations between variants on a gene regulatory pathways and a given phenotype
Version 0.1.0

geneticsCRE is an R package that performs pathway-based genome-wide association study (PGWAS) to identify statistically significant associations between variants on a gene regulatory pathways and a given phenotype. Unlike Genome-wide association study (GWAS), that seeks to assign statistical significance to associations of variations in single genes to a phenotype, PGWAS accumulates statistical power by examining rare variant along gene-gene interaction pathways. PGWAS uses prior causal information a gene regulatory interactions to infer statistically significant associations between causal pathways and a the phenotype. Given phenotype data with case/control information, geneticsCRE computes PGWAS for all valid pathways as identified by the Homo Sapien STRINGdb causal network. Examples on usage are provided in the vignette.

Getting started

Package details

AuthorCarl Tony Fakhry and Kourosh Zarringhalam
MaintainerCarl Tony Fakhry <[email protected]>
LicenseGPL (>=3)
Version0.1.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("carltonyfakhry/geneticsCRE")
carltonyfakhry/geneticsCRE documentation built on Oct. 1, 2017, 1:11 a.m.