Thanks for doing this. Getting an error with minifi::mapToGenome

[jsevo]

Following the minifi instructions, then applying as per the README:

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

yields an error when using mapToGenome:

GRset <- mapToGenome(RSet)

Loading required package: IlluminaMouseMethylationanno.12.v1.mm10 Error in getAnnotationObject(object) : cannot load annotation package IlluminaMouseMethylationanno.12.v1.mm10 In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘IlluminaMouseMethylationanno.12.v1.mm10’

[chiaraherzog]

Hi,

thanks for your message! Can I check that you also have IlluminaMouseMethylationanno12.v1.mm10 installed and loaded in?

For human packages, there are also two packages (manifest and annotation) but typically one is loaded in 'under the hood' if it's not present yet. I have added a pull request to minfi for the mouse packages to be included but it has not yet been added.

For me this code executes without errors (with the Illumina Mouse demo set from here:

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

RGset <- read.metharray.exp("~/Downloads/mousedemo/Infinium Mouse Methylation Demo Dataset/",
                            recursive = T)

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

Mset <- preprocessRaw(RGset)
Rset <- ratioConvert(Mset)
GRset <- mapToGenome(Rset)

Let me know if adding the additional package works. I'll think about adding a dependence for the other package when downloading one of the mouse packages.

Best,
Chiara

[chiaraherzog]

Hi @jsevo - just wanted to check whether you had any issues or comments? I'd like to close this issue.

Best,
Chiara

[jsevo]

I'll double check next week!

…

On Thu, Jul 11, 2024 at 5:09 AM Chiara Herzog ***@***.***> wrote: Hi @jsevo <https://github.com/jsevo> - just wanted to check whether you had any issues or comments? I'd like to close this issue. Best, Chiara — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABMUEWQOQ2W2BEPOQDDRSFTZLZDWLAVCNFSM6AAAAABKWRKU46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRSGQYTQMRWGM> . You are receiving this because you were mentioned.Message ID: ***@***.*** com>

[chiaraherzog]

Hi @jsevo - any updates on this? :)