Performs mQTL (methylation quantitative-trait locus) mapping in
bisulfite sequencing studies by fitting a binomial mixed model and then
incorporating the allelic-specific methylation pattern. Based on Fan, Yue;
Vilgalys, Tauras P.; Sun, Shiquan; Peng, Qinke; Tung, Jenny; Zhou, Xiang
(2019)
mQTL mapping in bisulfite sequencing studies by fitting a binomial mixed model, incorporating allelic-specific methylation pattern.
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")
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)
All the results from all methods used in the PMR-Egger paper can be reproduced at https://github.com/3211895/IMAGEreproduce