R package AEenrich

Overview

Adverse event (AE) enrichment analysis. Unlike continuous gene expression data, AE data are counts. Therefore, AE data has many zeros and ties. We propose two enrichment tests, AEFisher is a modified Fisher’s exact test based on pre-selected significant AEs, while AEKS is based on a modified Kolmogorov-Smirnov statistic.

Install from CRAN

install.packages("AEenrich")

Then, load the package with

library(AEenrich)

Install from Github

If the devtools package is not yet installed, install it first:

install.packages('devtools')

Then run:

# install AEenrich from Github:
devtools::install_github('umich-biostatistics/AEenrich') 
library(AEenrich)

Example usage

For documentation pages:

?AEenrich
?enrich

Quick example:

##---Experiment 1 
drug.case = 'FLUN'
drug.control = 'FLU'

# AEKS
## Data Type 1
KS_result1 = enrich(df = flu1, dd.group = group, drug.case = drug.case, 
                    drug.control = drug.control, method = 'aeks', n_iter = 1000)
## Data Type 2
KS_result2 = enrich(df = flu2, dd.group = group, drug.case = drug.case, 
                    drug.control = drug.control, method = 'aeks', n_iter = 1000)

# AEFisher
## Data Type 1
fisher_result1 = enrich(df = flu1, dd.group = group, drug.case = drug.case, 
                        drug.control = drug.control, method = 'aefisher', 
                        n_iter = 1000, q.cut = 0.1, or.cut=1.5)
## Data Type 2
fisher_result2 = enrich(df = flu2, dd.group = group, drug.case = drug.case, 
                        drug.control = drug.control, method = 'aefisher', 
                        n_iter = 1000, q.cut = 0.1, or.cut=1.5)

Current Suggested Citation

Li, S. and Zhao, L. (2020). Adverse event enrichment tests using VAERS. arXiv:2007.02266.