dnaEPICO: DNA methylation preprocessing and modeling workflows

dnaEPICO provides workflows for preprocessing and analyzing Illumina DNA methylation arrays. It supports quality control, normalization, cell-type estimation, surrogate-variable analysis, phenotype preparation, CpG-wise generalised linear models, longitudinal mixed-effects models using lmerTest/lme4 or nlme, and web reporting.

Details

The package supports two usage styles:

• interactive use, where functions return structured in-memory result objects for inspection and composition; and

• file-based pipeline use, where the same functions can write logs, plots, tables, and serialized objects when saveOutputs = TRUE.

The main high-level entry points are:

• preprocessingMinfiEwasWater()

• svaEnmix()

• preprocessingPheno()

• methylationGLM()

• methylationLME()

• dnamReport()

See also

Useful links:

• https://github.com/paulYRP/dnaEPICO

• Report bugs at https://github.com/paulYRP/dnaEPICO/issues

Author

Maintainer: Paul Ruiz Pinto ruizpint@qut.edu.au (ORCID)

Authors:

• Paul Ruiz Pinto ruizpint@qut.edu.au (ORCID)