export-tracks {rtracklayer}R Documentation

Export tracks

Description

These functions output trackSet instances in various formats.

Usage

export.gff(object, con, version = c("1", "2", "3"), source =
           "rtracklayer")
export.gff1(object, con, ...)
export.gff2(object, con, ...)
export.gff3(object, con, ...)
export.bed(object, con, wig = FALSE, color = NULL, ...)
export.wig(object, con,
           dataFormat = c("auto", "bed", "variableStep", "fixedStep"), ...)
export.ucsc(object, con, subformat = c("auto", "gff1", "wig", "bed"), ...)

Arguments

object The object to export, such as a trackSet. If a ucscTrackSet, the track line information is output. In the case of export.ucsc, a trackSets object with possibly multiple tracks is supported.
con The connection to which the object is exported.
version The GFF version, either "1", "2" or "3" (default is "1").
source The source of the GFF information, for GFF.
wig Whether to output the WIG variant of BED lines, not to be used directly.
color Recycled vector of colors, as interpreted by col2rgb for BED features. If NULL, the color column in the featureData is used, if any.
dataFormat The format of the data lines for WIG tracks, see references. The "auto" format uses the most efficient format possible.
subformat The format of the tracks within the UCSC container. If "auto", "wig" is used for numeric data, else "bed".
... For export.gff1, export.gff2 and export.gff3: arguments to pass to export.gff. For export.bed and export.wig : arguments to pass to methods. For export.ucsc: arguments to pass to export.subformat or to set on the slots of the ucscTrackLine subclass corresponding to subformat.

Value

If con is missing, a character vector containing the string output, otherwise nothing.

Author(s)

Michael Lawrence

References

GFF1 and GFF2
http://www.sanger.ac.uk/Software/formats/GFF
GFF3
http://www.sequenceontology.org/gff3.shtml
BED
http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
WIG
http://genome.ucsc.edu/goldenPath/help/wiggle.html
UCSC
http://genome.ucsc.edu/goldenPath/help/customTrack.html

See Also

See export for the high-level interface to these functions.

Examples

  dummy <- file() # dummy file connection for demo
  track <- import(system.file("tests", "bed.wig", package = "rtracklayer"))
  ## output a track as GFF2
  export.gff(track, dummy, version = "2")
  ## equivalently
  export.gff2(track, dummy)
  ## output as WIG string in variableStep format
  wig <- export.wig(track, dummy, dataFormat = "variableStep")
  ## output multiple tracks in UCSC meta-format
  track2 <- import(system.file("tests", "v1.gff", package = "rtracklayer"))
  ## output to WIG with BED line format
  export.ucsc(trackSets(track, track2), dummy, subformat = "wig", dataFormat = "bed") 

[Package rtracklayer version 1.2.2 Index]