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.
|Author||Barfield, R., Conneely, K., Kilaru,V|
|Date of publication||2016-01-29 22:22:21|
|Maintainer||R Barfield <email@example.com>|
|License||GPL (>= 2)|
cpg: Methods for object of class '"cpg"'
cpg.assoc: Association Analysis Between Methylation Beta Values and...
CpGassoc-package: Association Between Methylation and a Phenotype of Interest
cpg.combine: Combine various objects of class '"cpg"'
cpg.everything: Multi-Task function
cpg.GC: cpg.GC and methods for output of function
cpg.perm: Perform a Permutation Test of the Association Between...
cpg.perm.object: Methods for object of class '"cpg.perm"'.
cpg.qc: Performs quality control on Illumina data.
cpg.work: Does the analysis between the CpG sites and phenotype of...
design: Create full and reduced design matrices for the cpg.assoc...
manhattan: Create a manhattan plot
manhattan.reflect: Create a Reflective Manhattan plot
other.functions: Information on miscellaneous other functions
Sample.data: Sample data from 'CpGassoc'
scatterplot: Plot beta values of individual CpG sites against the...