Add generate Annotation function to bigmelon

[TJGorrie]

Use the codes I use all the time to generate, EPIC or 450k annotations, optionally add them to gds file.

You can generate the fData like this

annoObj <-  minfi::getAnnotationObject("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
all <- minfi:::.availableAnnotation(annoObj)$defaults
newfData <- do.call(cbind, lapply(all, function(wh) {
        minfi:::.annoGet(wh, envir = annoObj@data)
}))
newfData <- newfData[rownames(gfile), ] # SNP probes will be missing, and be NA’d I think.
rownames(newfData) <- rownames(gfile)

And add it with:

# If the gfile was opened with openfn.gds(..., readonly=FALSE)
add.gdsn(gfile, name='fData', val = newfData, replace = TRUE)