GenomeAnnotatedDataFrame-class {oligoClasses} | R Documentation |
"GenomeAnnotatedDataFrame"
AnnotatedDataFrame with genomic coordinates (chromosome, position)
varMetadata
:Object of class "data.frame"
~~
data
:Object of class "data.frame"
~~
dimLabels
:Object of class "character"
~~
.__classVersion__
:Object of class "Versions"
~~
Class "AnnotatedDataFrame"
, directly.
Class "Versioned"
, by class "AnnotatedDataFrame", distance 2.
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
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).
R. Scharpf