| UCSCData-class {rtracklayer} | R Documentation |
Each track in UCSC has an associated
TrackLine that contains metadata on the track.
trackLine:"TrackLine"
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. 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. as(object, "UCSCData")UCSCData
from a RangedData instance, by adding a default track line
and ensuring that the sequence/chromosome names are compliant with
UCSC conventions.
Michael Lawrence
import and export for reading and writing
tracks to and from connections (files), respectively.