GenomeAnnotatedDataFrame-class {oligoClasses} | R Documentation

## Class `"GenomeAnnotatedDataFrame"`

### Description

AnnotatedDataFrame with genomic coordinates (chromosome, position)

### Slots

`varMetadata`:

  Object of class `"data.frame"` ~~

`data`:

  Object of class `"data.frame"` ~~

`dimLabels`:

  Object of class `"character"` ~~

`.__classVersion__`:

  Object of class `"Versions"` ~~

### Extends

Class `"AnnotatedDataFrame"`, directly. Class `"Versioned"`, by class "AnnotatedDataFrame", distance 2.

### Coercion to or from other classes

  `as(from, "GenomeAnnotatedDataFrame")`:

  Coerce an object of class `AnnotatedDataFrame` to a `GenomeAnnotatedDataFrame`.

  `makeFeatureGRanges(object, genome, ...)`:

  Construct a `GRanges` instance from a `GenomeAnnotatedDataFrame` object. `genome` is a character string indicating the UCSC build. Supported builds are "hg18" and "hg19", but are platform specific. In particular, some platforms only support build hg19 at this time.

  `updateObject(object)`:

  For updating a `GenomeAnnotatedDataFrame`

### Accessors

  `chromosome(object)`, `chromosome(object) <- value`

  Get or set chromosome.

  `isSnp(object)`:

  Many platforms include polymorphic and nonpolymorphic markers. isSnp evalutes to `TRUE` if the marker is polymorphic.

  `position(ojbect)`:

  Physical position in the genome

  `getArm(object, genome)`:

  Retrieve character vector indicating the chromosome arm of each marker in `object`. `genome` should indicate which genome build was used to define the chromosomal locations (currently, only UCSC genome builds 'hg18' and 'hg19' supported for this function).

### Author(s)

R. Scharpf

### See Also

`AnnotatedDataFrame`

### Examples

    new("GenomeAnnotatedDataFrame")
    if(require("pd.mapping50k.hind240") && require("pd.mapping50k.xba240") && require("SNPchip")){
    	data(locusLevelData)
    	gd <- GenomeAnnotatedDataFrameFrom(locusLevelData[["genotypes"]],
    					       annotationPkg=locusLevelData[["platform"]],
    					       genome="hg19")
            arm <- getArm(gd, "hg19")
    }

[Package oligoClasses version 1.42.0 Index]