GenomeAnnotatedDataFrame-class: Class '"GenomeAnnotatedDataFrame"'

In benilton/oligoClassesOld: Classes for high-throughput arrays supported by oligo and crlmm

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")
}

benilton/oligoClassesOld documentation built on May 12, 2019, 11:51 a.m.