README.md

In DavisBrian/gwasr: Provide a framework to make GWAS easier.

gwasr

The aim of gwasr is to provide common structures and interface for conducting GWAS (Genome-Wide Association Studies). gwasr provides a robust set of tools to interface with various GWAS testing methods and eliminate (or at least catch early) common analysis mistakes. The main goal of gwar is to allow analyst greater focus on the analysis at hand and reduce focus from the nuances of the underlying data manipulation.

Fundamentally gwasr is a set of tools for a common set of problems. split the genotypes into individual snps or genes (or gene like structures), apply a test or calculate a metric (T1, SKAT, regression, etc), and combine the results back together.

Effort has been put into making gwasr fast and memory efficient.

Installation

gwasr is currently not on CRAN, but you can get it from github with:

# install.packages("devtools")
devtools::install_github("DavisBrian/gwasr")

Learning gwasr

[TBD] - Vignettes

Key structures

The key objects in gwasr are:

• phenotype
• genotypes
• snpinfo

Single Object Verbs

• summary

Multi Object Verbs

Usage / Examples

The following example uses gwasr to solve a fairly realistic problem: With phenotype, genotype, and a snpinfo file for each "gene", run a T5 test.

[TBD]

Future plans

DavisBrian/gwasr documentation built on May 6, 2019, 1:55 p.m.