Association Between Methylation and a Phenotype of Interest
Multi-Task function
Association Analysis Between Methylation Beta Values and Phenotype of ...
Combine various objects of class "cpg"
cpg.GC and methods for output of function
Methods for object of class "cpg.perm".
Perform a Permutation Test of the Association Between Methylation and ...
Performs quality control on Illumina data.
Methods for object of class "cpg"
Does the analysis between the CpG sites and phenotype of interest
Association Between Methylation and a Phenotype of Interest
Create full and reduced design matrices for the cpg.assoc function.
Create a manhattan plot
Create a Reflective Manhattan plot
Information on miscellaneous other functions
Sample data from CpGassoc
Plot beta values of individual CpG sites against the independent varia...
Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.