Although they primarily contain annotation rather than code, these can be treated like R software packages. Hopefully at some point in the future they will be included in Bioconductor and you will be able to use biocLite() to install them.
However, for now you can install straight from the downloaded tar.gz file. If you use RStudio then you can do:
Install Packages ->
Install From "Package Archive File (tar.gz)" ->
Select the tar.gz file
If you are working at the command line then you can run something like the following in a terminal:
R CMD INSTALL /path/to/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz
Have another question and I have to apologise if this sounds like a silly question to ask (new to all of this)
So I've installed the two packages so does that mean when I run minfi it will automatically use the EPIC manifest and anno or will it use the 450k ones? Is there a command I need to use to run the EPIC files in R?
Also I'm going through the minfi tutorial using the minfiData package and I guess its written up for the 450K array. So just wanted to know again when I run minfi using my data files will it use the EPIC manifest etc. I am a bit confused because in the tutorial the RGchannel set is set for the 450K.