README.Rmd

---
title: "IlluminaMouseMethylationanno.12.v1.mm10"
author: "Chiara Herzog"
date: "19/08/2022"
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 using 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 IlluminaMouseMethylationmanifest package.

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

# Installation

```
if(!require(devtools)) install.packages("devtools")
devtools::install_github("chiaraherzog/IlluminaMouseMethylationanno.12.v1.mm10")
```

# Requirements

R >= 4.1.2, uses minfi (>= 1.40.0)

# Use

Annotation can be obtained as follows:

```
data <- getAnnotation(IlluminaMouseMethylationanno.12.v1.mm10)
```

The manifest - using the IlluminaMouseMethylationmanifest package (chiaraherzog/IlluminaMouseMethylationmanifest) - can be applied after an RGset has been created with minfi:

```
library(IlluminaMouseMethylationanno.12.v1.mm10)
library(IlluminaMouseMethylationmanifest)

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

# Helper functions

The package includes a helper function for DMRcate (cpg.annotate), that can be used as follows (example) on a beta matrix:

```
library(DMRcate)
myannotation <- IlluminaMouseMethylationanno.12.v1.mm10::cpg.annotate("array", beta,
                             arraytype = "mouse",
                             analysis.type="differential", design=design, coef=2)
dmr <- DMRcate::dmrcate(myannotation)
```

where design represents a design model matrix.