Hi,

I am fairly new to R programming and using Bioconductor packages. I am trying to install  IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz and IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.3.0.tar.gz which I downloaded from https://bitbucket.org/hansenlab/illumina_epic. I read that we need to install it using the cd prompt but I'm finding it really hard to install it that way. I cant find the install or a readme file which has the instructions.

Would be great if a step by step guide can be given from point of download to installing the package in R can be given.

Any help is appreciated..

Thanks,

Rasi

These are available in R-3.3.0 / Bioc 3.3

> pp = available.packages(repos=BiocInstaller::biocinstallRepos()[2])
> grep("EPIC", rownames(pp), value=TRUE)
[1] "IlluminaHumanMethylationEPICanno.ilm10b2.hg19"
[2] "IlluminaHumanMethylationEPICmanifest"  
> BiocInstaller::biocVersion()
[1] '3.3'
> R.version.string
[1] "R version 3.3.0 alpha (2016-03-30 r70401)"

The landing pages are at, e.g., https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest . Once using the correct version of R, they install with

source("https://bioconductor.org/biocLIte.R")
biocLIte("IlluminaHumanMethylationEPICmanifest")

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:

Tools ->

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

Thanks so much guys! Managed to install them...now to work out how to use it to analyze my .idat files..

Rasi

Hi guys,

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.

Thanks again