| 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.