ucscTrackSet-class {rtracklayer} | R Documentation |
Each track in UCSC has an associated
ucscTrackLine
that contains metadata on the track.
Objects can be created by calls of the form new("ucscTrackSet",
assayData, phenoData, featureData, experimentData, annotation,
...)
. See trackSet
for more details.
trackLine
:"ucscTrackLine"
holding track metadata. genome
:"character"
identifying
the genome of this track, e.g. "hg18".assayData
:"AssayData"
holding
the experimental measurements under dataVals
. phenoData
:"AnnotatedDataFrame"
holding the experimental design matrix. featureData
:"AnnotatedDataFrame"
holding feature information, generally
including columns chrom
(chromosome), start
(start position), end
(end position) and
strand
(strand on the DNA: "+", "-", or NA
).experimentData
:"MIAME"
holding
experimental metadata.annotation
:"character"
referring to the annotation dataset. .__classVersion__
:"Versions"
holding version information.
Class "trackSet"
, directly.
Class "eSet"
, by class "trackSet", distance 2.
Class "VersionedBiobase"
, by class "trackSet", distance 3.
Class "Versioned"
, by class "trackSet", distance 4.
export.bed(object, con, wig = FALSE, trackLine =
!wig)
trackLine
is TRUE
) to con
in the Browser
Extended Display (BED) format. export.gff(object)
con
in the
General Feature Format (GFF). export.ucsc(object)
con
in the
UCSC meta-format. Michael Lawrence
import
and export
for reading and writing
tracks to and from connections (files), respectively.