Association Between Methylation and a Phenotype of Interest

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Documentation for package ‘CpGassoc’ version 2.60

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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"'.