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.