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

Functions

annotation Man page
cpg.assoc Man page
CpGassoc Man page
CpGassoc-package Man page
cpgassocsummary Man page
cpg.combine Man page
cpg.everything Man page
cpg.everything.character Man page
cpg.everything.complex Man page
cpg.everything.logical Man page
cpg.everything.matrix Man page
cpg.everything.numeric Man page
cpg.GC Man page
cpg.length Man page
cpg.perm Man page
cpg.qc Man page
cpg.work Man page
design Man page
design.data.frame Man page
design.NULL Man page
manhattan Man page
manhattan.reflect Man page
plot.cpg Man page
plot.cpg.perm Man page
pointsizefunction Man page
print.cpg Man page
print.cpg.gc Man page
print.cpg.perm Man page
print.cpg.perm.gc Man page
samplecpg Man page
samplepheno Man page
scatterplot Man page
sort.cpg Man page
sort.cpg.perm Man page
summary.cpg Man page
summary.cpg.perm Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.