IMAGE

mQTL mapping in bisulfite sequencing studies by fitting a binomial mixed model, incorporating allelic-specific methylation pattern.

Installation

IMAGE requires the following R packages:

install.packages(c("foreach", "doParallel", "Matrix", "MASS"))

You can install the released version of IMAGE from CRAN with:

install.packages("IMAGE")

Or install the development version from:

library(devtools)
install_github("umich-biostatistics/IMAGE")

Usage

The main function is image. You can find the instructions and an example by ‘?image’.

Example:

data(ExampleData)
geno <- ExampleData$geno
K <- ExampleData$K
data <- ExampleData$data
res=image(geno,data,K)

Results Reproduced

All the results from all methods used in the PMR-Egger paper can be reproduced at https://github.com/3211895/IMAGEreproduce