README.md

In schalkwyk/wateRmelon: Illumina 450 and EPIC methylation array normalization and metrics

wateRmelon

Illumina 450 and EPIC methylation array normalization and metrics

Software status

| Resource: | Bioconductor (Release) | Bioconductor (Devel) | | ------------- | ------------------- | ------------- | | Platforms: | Multiple | Multiple | | R CMD check | |

Currently on Github I'm doing some maintenance, in particular in order to work with EPICv2 arrays. If you install:

https://github.com/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38

and

https://github.com/jokergoo/IlluminaHumanMethylationEPICv2manifest

.... as well as this version of wateRmelon, you can read in EPICv2 array IDAT files with wateRmelon and bigmelon.

Most functions including dasen and the other Pidsley et al 2013 normalisers, genki, dmrse, and agep work at least in wateRmelon but have only been superficially tested, additional testingand improvement is underway. Bug reports are welcome at [e-mail] or via github.

1. Installation

Install from Github

## Make sure 'devtools' is installed in your R
# install.packages("devtools")
devtools::install_github("schalkwyk/wateRmelon")

schalkwyk/wateRmelon documentation built on April 15, 2024, 12:06 p.m.