Association Between Methylation and a Phenotype of Interest

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Documentation for package ‘CpGassoc’ version 2.60

• 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"'.