R: Importing tracks

import.gff {rtracklayer}

R Documentation

Importing tracks

Description

These are the functions for importing RangedData instances from connections or text.

Usage

import.gff(con, version = c("1", "2", "3"), genome = NULL,
           asRangedData = TRUE, colnames = NULL)
import.gff1(con, ...)
import.gff2(con, ...)
import.gff3(con, ...)
import.bed(con, variant = c("base", "bedGraph", "bed15"),
           trackLine = TRUE, genome = NULL,
           asRangedData = TRUE, colnames = NULL, ...)
import.bed15(con, genome = NULL, asRangedData = TRUE, ...)
import.bedGraph(con, genome = NULL, asRangedData = TRUE, ...)
import.wig(con, genome = NULL, asRangedData = TRUE, ...)
import.ucsc(con,
            subformat = c("auto", "gff1", "wig", "bed", "bed15", "bedGraph"),
            drop = FALSE, asRangedData = TRUE, ...)
## not yet supported on Windows
import.bw(con, ...)

Arguments

`con`	The connection, filename or URL from which to receive the input.
`version`	The version of GFF ("1", "2" or "3").
`genome`	The genome to set on the imported track.
`asRangedData`	A logical value. If `TRUE`, a RangedData object is returned. If `FALSE`, a GRanges object is returned.
`variant`	Variant of BED lines, not for the user.
`trackLine`	Whether the BED data has a track line (it normally does though track lines are not mandatory).
`subformat`	The expected subformat of the UCSC data. If "auto", automatic detection of the subformat is attempted.
`drop`	If `TRUE` and there is only one track in the UCSC data, return the track instead of a list.
`colnames`	Character vector indicating which columns (excluding the required sequence name, start and end) should be imported. If `NULL`, all columns are imported. This allows some significant optimizations, especially when it is not necessary to import GFF attributes attributes, which are expensive to parse.
`...`	For `import.gff1`, `import.gff2` and `import.gff3`: arguments to pass to `import.gff`. For `import.ucsc`: arguments to pass on to `import.subformat`. For the others, arguments to pass to methods. See `BigWigFile` for additional arguments on `import.bw`.

Value

For all but import.ucsc, an instance of RangedData (or one of its subclasses) or GRanges if asRangedData is TRUE or FALSE respectively.

For import.ucsc when drop is FALSE, an instance of RangedDataList or GRangesList if asRangedData is TRUE or FALSE respectively.

Author(s)

Michael Lawrence and Patrick Aboyoun

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

Examples

  # import a GFF V2 file
  gffRD <- import.gff(system.file("tests", "v2.gff", package = "rtracklayer"),
                      version = "2")
  gffGR <- import.gff(system.file("tests", "v2.gff", package = "rtracklayer"),
                      version = "2", asRangedData = FALSE)
  # or
  gffRD <- import.gff2(system.file("tests", "v2.gff", package = "rtracklayer"))
  gffGR <- import.gff2(system.file("tests", "v2.gff", package = "rtracklayer"),
                       asRangedData = FALSE)

  # import a WIG file
  wigRD <- import.wig(system.file("tests", "bed.wig", package = "rtracklayer"))
  wigGR <- import.wig(system.file("tests", "bed.wig", package = "rtracklayer"),
                      asRangedData = FALSE)
  # or
  wigRD <- import.ucsc(system.file("tests", "bed.wig", package = "rtracklayer"),
                       subformat = "wig", drop = TRUE)
  wigGR <- import.ucsc(system.file("tests", "bed.wig", package = "rtracklayer"),
                       subformat = "wig", drop = TRUE, asRangedData = FALSE)

  # bigWig
## Not run: 
  bw <- import(system.file("tests", "test.bw", package = "rtracklayer"),
               ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7)))

## End(Not run)

[Package rtracklayer version 1.14.1 Index]