[Bioc-devel] Manifest and annotation packages for EPIC methylation array v2.0

Tue, Mar 21, 2023 1:35 PM

I am aware of the AnnotationHub package, but currently I think it is not
possible to integrate with minfi.

In the last several lines in
https://github.com/hansenlab/minfi/blob/master/R/IlluminaMethylationAnnotation-class.R

setMethod(
    "getManifest",
    signature(object = "IlluminaMethylationAnnotation"),
    function(object) {
        maniString <- .getManifestString(object at annotation)
        if (!require(maniString, character.only = TRUE)) {
            stop(sprintf("cannot load manifest package %s", maniString))
        }
        get(maniString)
    }
)

Here `maniString` contains the name of a manifest package,
e.g. IlluminaHumanMethylationEPICmanifest. After loading the manifest
package, minfi directly looks for the variable with the same name as the
manifest package name. So it would be the easiest if just making a new
manifest package taking the IlluminaHumanMethylationEPICmanifest as a
template. Or minfi needs to be adjusted to allow for more flexible
integration of new manifest packages/objects.

Cheers,
Zuguang

On Tue, 21 Mar 2023 at 14:58, Kern, Lori <Lori.Shepherd at roswellpark.org>
wrote:

_______________________________________________
Bioc-devel at r-project.org mailing list

https://secure-web.cisco.com/1fLuxP9yMKjXXVX4U5tHzgq75S4SiNaqqCjLqVieInk0UcUFlM9Awx7EvllsKfkmUEniVGH9qtKoo7YszKjXKiEqBmS-SnNM5_w5UYUkpy_dra04LGCCNrmlmTbGxHsBYUbisl9F6Yap5oDm92TIPyqi1KON0yYy85JJ0laeEbH6hsT4RUGa7NgW2PBNm7lUnl0z7ryA7jU-y2g0Vxq4r43sbbuCtkxrL23V_MwiMsRq3ekTwtHudDEoUNxJurdguVYJRzxPP4Ji4f7U5SucexI2cYfMIDl2e3Puple98Zuo9MxVTEYXpZ-nLJgqVe7LS/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel


This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.

[Bioc-devel] Manifest and annotation packages for EPIC methylation array v2.0

Thread (3 messages)