README.Rmd

---
title: "IlluminaMouseMethylationmanifest readme"
author: "Chiara Herzog"
date: "16/08/2022"
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

This R package was create for analysis of Illumina Mouse Methylation Array datasets with minfi. The annotation was downloaded from Illumina (accessed 12 Aug 2022) and follows the development of IlluminaMethylationEPIC packages.
It is to be used in combination with the IlluminaMouseMethylationanno.12.v1.mm10 package.

As several CpGs have multiple probes, Illumina IDs concatenated from cgID and additinal information are used rather than cg numbers on their own.

The manifest can be applied after an RGset has been created with minfi:

```{r eval=F}
library(IlluminaMouseMethylationanno.12.v1.mm10)
library(IlluminaMouseMethylationmanifest)

RGset@annotation <-  c(array = "IlluminaMouseMethylation", annotation = "12.v1.mm10")
```