Package: CpGassoc 2.70

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.

Authors:Barfield, R., Conneely, K., Kilaru,V

CpGassoc_2.70.tar.gz
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CpGassoc.pdf |CpGassoc.html✨
CpGassoc/json (API)

# Install 'CpGassoc' in R:

install.packages('CpGassoc', repos = c('https://rbarfield.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

annotation - Sample data from 'CpGassoc'
samplecpg - Sample data from 'CpGassoc'
samplepheno - Sample data from 'CpGassoc'

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.68 score 48 scripts 373 downloads 26 mentions 31 exports 2 dependencies

Last updated 4 months agofrom:639c1717c8. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 18 2024
R-4.5-win	OK	Oct 18 2024
R-4.5-linux	OK	Oct 18 2024
R-4.4-win	OK	Oct 18 2024
R-4.4-mac	OK	Oct 18 2024
R-4.3-win	OK	Oct 18 2024
R-4.3-mac	OK	Oct 18 2024

Exports:cpg.assoc cpg.combine cpg.everything cpg.everything.character cpg.everything.complex cpg.everything.logical cpg.everything.matrix cpg.everything.numeric cpg.GC cpg.length cpg.perm cpg.qc cpg.work cpgassocsummary design design.data.frame design.NULL manhattan manhattan.reflect plot.cpg plot.cpg.perm pointsizefunction print.cpg print.cpg.gc print.cpg.perm print.cpg.perm.gc scatterplot sort.cpg sort.cpg.perm summary.cpg summary.cpg.perm

Dependencies:lattice nlme

CpGassoc reference

Rendered fromCpGassoc.Rnwusingutils::Sweaveon Oct 18 2024.

Last update: 2024-07-17
Started: 2013-09-16

Help page	Topics
Association Between Methylation and a Phenotype of Interest	CpGassoc-package CpGassoc
Methods for object of class '"cpg.perm"'.	plot.cpg.perm print.cpg.perm sort.cpg.perm summary.cpg.perm
Methods for object of class '"cpg"'	plot.cpg print.cpg sort.cpg summary.cpg
Association Analysis Between Methylation Beta Values and Phenotype of Interest	cpg.assoc
Combine various objects of class '"cpg"'	cpg.combine
Multi-Task function	cpg.everything cpg.everything.character cpg.everything.complex cpg.everything.logical cpg.everything.matrix cpg.everything.numeric
cpg.GC and methods for output of function	cpg.GC print.cpg.gc print.cpg.perm.gc
Perform a Permutation Test of the Association Between Methylation and a Phenotype of Interest	cpg.perm
Performs quality control on Illumina data.	cpg.qc
Does the analysis between the CpG sites and phenotype of interest	cpg.work
Create full and reduced design matrices for the cpg.assoc function.	design design.data.frame design.NULL
Create a manhattan plot	manhattan
Create a Reflective Manhattan plot	manhattan.reflect
Information on miscellaneous other functions	cpg.length cpgassocsummary pointsizefunction
Sample data from 'CpGassoc'	annotation samplecpg samplepheno
Plot beta values of individual CpG sites against the independent variable.	scatterplot

Package: CpGassoc 2.70

CpGassoc: Association Between Methylation and a Phenotype of Interest

CpGassoc reference

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)