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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

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Version

Install

install.packages('IMAGE')

Version

1.0

License

GPL-2

Last Published

July 28th, 2019

Functions in IMAGE (1.0)

image

High-powered detection of genetic effects on DNA methylation
ExampleData

Example data set to test the IMAGE method
example_results

Example results using the example data set