# Association Between Methylation and a Phenotype of Interest

## Documentation for package ‘CpGassoc’ version 2.70

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

CpGassoc-package | Association Between Methylation and a Phenotype of Interest
annotation | Sample data from 'CpGassoc'
cpg.assoc | Association Analysis Between Methylation Beta Values and Phenotype of Interest
cpg.combine | Combine various objects of class '"cpg"'
cpg.everything | Multi-Task function
cpg.everything.character | Multi-Task function
cpg.everything.complex | Multi-Task function
cpg.everything.logical | Multi-Task function
cpg.everything.matrix | Multi-Task function
cpg.everything.numeric | Multi-Task function
cpg.GC | cpg.GC and methods for output of function
cpg.length | Information on miscellaneous other functions
cpg.perm | Perform a Permutation Test of the Association Between Methylation and a Phenotype of Interest
cpg.qc | Performs quality control on Illumina data.
cpg.work | Does the analysis between the CpG sites and phenotype of interest
CpGassoc | Association Between Methylation and a Phenotype of Interest
cpgassocsummary | Information on miscellaneous other functions
design | Create full and reduced design matrices for the cpg.assoc function.
design.data.frame | Create full and reduced design matrices for the cpg.assoc function.
design.NULL | Create full and reduced design matrices for the cpg.assoc function.
manhattan | Create a manhattan plot
manhattan.reflect | Create a Reflective Manhattan plot
plot.cpg | Methods for object of class '"cpg"'
plot.cpg.perm | Methods for object of class '"cpg.perm"'.
pointsizefunction | Information on miscellaneous other functions
print.cpg | Methods for object of class '"cpg"'
print.cpg.gc | cpg.GC and methods for output of function
print.cpg.perm | Methods for object of class '"cpg.perm"'.
print.cpg.perm.gc | cpg.GC and methods for output of function
samplecpg | Sample data from 'CpGassoc'
samplepheno | Sample data from 'CpGassoc'
scatterplot | Plot beta values of individual CpG sites against the independent variable.
sort.cpg | Methods for object of class '"cpg"'
sort.cpg.perm | Methods for object of class '"cpg.perm"'.
summary.cpg | Methods for object of class '"cpg"'
summary.cpg.perm | Methods for object of class '"cpg.perm"'.