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.

AuthorBarfield, R., Conneely, K., Kilaru,V
Date of publication2016-01-29 22:22:21
MaintainerR Barfield <rbarfield01@fas.harvard.edu>
LicenseGPL (>= 2)
Version2.55

View on CRAN

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

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