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
CpGassoc_2.70.zip(r-4.5)CpGassoc_2.70.zip(r-4.4)CpGassoc_2.70.zip(r-4.3)
CpGassoc_2.70.tgz(r-4.4-any)CpGassoc_2.70.tgz(r-4.3-any)
CpGassoc_2.70.tar.gz(r-4.5-noble)CpGassoc_2.70.tar.gz(r-4.4-noble)
CpGassoc_2.70.tgz(r-4.4-emscripten)CpGassoc_2.70.tgz(r-4.3-emscripten)
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'))

Peer review:

Datasets:

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 381 downloads 26 mentions 31 exports 2 dependencies

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

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-winOKNov 17 2024
R-4.5-linuxOKNov 17 2024
R-4.4-winOKNov 17 2024
R-4.4-macOKNov 17 2024
R-4.3-winOKNov 17 2024
R-4.3-macOKNov 17 2024

Exports:cpg.assoccpg.combinecpg.everythingcpg.everything.charactercpg.everything.complexcpg.everything.logicalcpg.everything.matrixcpg.everything.numericcpg.GCcpg.lengthcpg.permcpg.qccpg.workcpgassocsummarydesigndesign.data.framedesign.NULLmanhattanmanhattan.reflectplot.cpgplot.cpg.permpointsizefunctionprint.cpgprint.cpg.gcprint.cpg.permprint.cpg.perm.gcscatterplotsort.cpgsort.cpg.permsummary.cpgsummary.cpg.perm

Dependencies:latticenlme

CpGassoc reference

Rendered fromCpGassoc.Rnwusingutils::Sweaveon Nov 17 2024.

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