getAnnotation {minfi} | R Documentation

## Accessing annotation for Illumina methylation objects

### Description

These functions access provided annotation for various Illumina methylation objects.

### Usage

    getAnnotation(object, what = "everything", lociNames = NULL,
                  orderByLocation = FALSE, dropNonMapping = FALSE)

    getLocations(object, mergeManifest = FALSE,
                 orderByLocation = FALSE, lociNames = NULL)

    getAnnotationObject(object)

    getSnpInfo(object, snpAnno = NULL)
    addSnpInfo(object, snpAnno = NULL)

    dropLociWithSnps(object, snps = c("CpG", "SBE"), maf = 0, snpAnno = NULL)

    getProbeType(object, withColor = FALSE)

    getIslandStatus(object, islandAnno = NULL)

### Arguments

`object` | A `minfi` object.
`what` | Which annotation objects should be returned?
`lociNames` | Restrict the return values to these loci.
`orderByLocation` | Should the return object be ordered according to genomic location.
`dropNonMapping` | Should loci that do not have a genomic location associated with it (by being marked as `unmapped` or `multi`) be dropped from the return object.
`mergeManifest` | Should the manifest be merged into the return object?
`snpAnno` | The snp annotation you want to use; `NULL` signifies picking the default.
`withColor` | Should the return object have the type I probe color labelled?
`snps` | The type of SNPs used.
`maf` | Minor allelle fraction.
`islandAnno` | Like `snpAnno`, but for islands.

### Details

`getAnnotation` returns requested annotation as a `DataFrame`, with each row corresponding to a methylation loci. If `object` is of class `IlluminaHumanAnnotation` no specific ordering of the return object is imposed. If, on the other hand, the class of `object` imposes some natural order on the return object (ie. if the object is of class `[Genomic](Methyl|Ratio)Set`), this order is kept in the return object. Note that `RGChannelSet` does not impose a specific ordering on the methylation loci.

`getAnnotationObject` returns the annotation object, as opposed to the annotation the object contains. This is useful for printing and examining the contents of the object.

`getLocations` is a convenience function which returns `Locations` as a `GRanges` and which furthermore drops unmapped loci. A user should not need to call this function, instead `mapToGenome` should be used to get genomic coordinates and `granges` to return those coordinates.

`getSnpInfo` is a conevnience function which gets a SNP DataFrame containing information on which probes contains SNPs where. `addSnpInfo` adds this information to the `rowRanges` or `granges` of the object. `dropLociWithSnps` is a convenience function for removing loci with SNPs based on their MAF.

To see which options are available for `what`, simply print the annotation object, possibly using `getAnnotationObject`.

### Value

For `getAnnotation`, a `DataFrame` with the requested information.

For `getAnnotationObject`, a `IlluminaMethylationAnnotation` object.

For `getLocations`, a `GRanges` with the locations.

For `getProbeType` and `getIslandStatus`, a `character` vector with the requested information.

For `getSnpInfo`, a `DataFrame` with the requested information. For `addSnpInfo`, an object of the same class as `object` but with the SNP information added to the metadata columns of the granges of the object.

For `dropLociWithSnps` an object of the same kind as the input, possibly with fewer loci.

### Author(s)

Kasper Daniel Hansenkhansen@jhsph.edu

### See Also

`IlluminaMethylationAnnotation` for the basic class, `mapToGenome` for a better alternative (for users) to `getLocations`.

### Examples

    if(require(minfiData)) {
      table(getIslandStatus(MsetEx))
      getAnnotation(MsetEx, what = "Manifest")
    }

[Package minfi version 1.30.0 Index]