CpGassoc: Association Between Methylation and a Phenotype of Interest

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 <rbarfield01@fas.harvard.edu>
License
GPL (>= 2)
Version
2.55

View on CRAN

Man pages

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...

Files in this package

CpGassoc
CpGassoc/inst
CpGassoc/inst/doc
CpGassoc/inst/doc/CpGassoc.R
CpGassoc/inst/doc/CpGassoc.Rnw
CpGassoc/inst/doc/CpGassoc.pdf
CpGassoc/NAMESPACE
CpGassoc/data
CpGassoc/data/samplepheno.rda
CpGassoc/data/annotation.rda
CpGassoc/data/datalist
CpGassoc/data/samplecpg.rda
CpGassoc/R
CpGassoc/R/manhattan.reflect.R
CpGassoc/R/cpg.everything.complex.R
CpGassoc/R/cpg.assoc.R
CpGassoc/R/cpgassocsummary.R
CpGassoc/R/sort.cpg.perm.R
CpGassoc/R/cpg.everything.character.R
CpGassoc/R/cpg.everything.matrix.R
CpGassoc/R/cpg.combine.R
CpGassoc/R/sort.cpg.R
CpGassoc/R/print.cpg.gc.R
CpGassoc/R/CpGassoc-internal.R
CpGassoc/R/pointsizefunction.R
CpGassoc/R/cpg.length.R
CpGassoc/R/plot.cpg.perm.R
CpGassoc/R/print.cpg.perm.R
CpGassoc/R/design.NULL.R
CpGassoc/R/cpg.perm.R
CpGassoc/R/cpg.work.R
CpGassoc/R/plot.cpg.R
CpGassoc/R/cpg.everything.numeric.R
CpGassoc/R/scatterplot.R
CpGassoc/R/design.R
CpGassoc/R/cpg.everything.logical.R
CpGassoc/R/print.cpg.R
CpGassoc/R/print.cpg.perm.gc.R
CpGassoc/R/summary.cpg.R
CpGassoc/R/manhattan.R
CpGassoc/R/cpg.everything.R
CpGassoc/R/cpg.qc.R
CpGassoc/R/cpg.GC.R
CpGassoc/R/design.data.frame.R
CpGassoc/R/summary.cpg.perm.R
CpGassoc/vignettes
CpGassoc/vignettes/CpGassoc.Rnw
CpGassoc/MD5
CpGassoc/build
CpGassoc/build/vignette.rds
CpGassoc/DESCRIPTION
CpGassoc/man
CpGassoc/man/cpg.everything.Rd
CpGassoc/man/cpg.perm.Rd
CpGassoc/man/manhattan.reflect.Rd
CpGassoc/man/cpg.qc.Rd
CpGassoc/man/cpg.perm.object.Rd
CpGassoc/man/Sample.data.Rd
CpGassoc/man/cpg.Rd
CpGassoc/man/manhattan.Rd
CpGassoc/man/CpGassoc-package.Rd
CpGassoc/man/design.Rd
CpGassoc/man/cpg.work.Rd
CpGassoc/man/cpg.assoc.Rd
CpGassoc/man/cpg.GC.Rd
CpGassoc/man/cpg.combine.Rd
CpGassoc/man/scatterplot.Rd
CpGassoc/man/other.functions.Rd