| import.gff {rtracklayer} | R Documentation |
These are the functions for importing RangedData
instances from connections or text.
import.gff(con, version = c("1", "2", "3"), genome = "hg18")
import.gff1(con, ...)
import.gff2(con, ...)
import.gff3(con, ...)
import.bed(con, wig = FALSE, trackLine = !wig, genome = "hg18", ...)
import.wig(con, genome = "hg18", ...)
import.ucsc(con, subformat = c("auto", "gff1", "wig", "bed"),
drop = FALSE, ...)
con |
The connection from which to receive the input. |
version |
The version of GFF ("1", "2" or "3"). |
genome |
The genome to set on the imported track. |
wig |
Whether the BED lines are expected to be WIG formatted (not for public use). |
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. |
... |
For import.gff1, import.gff2 and
import.gff3: arguments to pass to import.gff. For
import.bed and import.wig: arguments to pass to methods.
For import.ucsc: arguments to pass on to import.subformat. |
An instance of RangedData or one of its subclasses,
except for import.ucsc, which returns a
RangedDataList instance, unless there is one track and
the drop parameter is TRUE.
Michael Lawrence
import for the high-level interface to these routines.
# import a GFF V2 file
gff <- import.gff(system.file("tests", "v2.gff", package = "rtracklayer"), version = "2")
# or
gff <- import.gff2(system.file("tests", "v2.gff", package = "rtracklayer"))
# import a WIG file
wig <- import.wig(system.file("tests", "bed.wig", package = "rtracklayer"))
# or
wig <- import.ucsc(system.file("tests", "bed.wig", package = "rtracklayer"),
subformat = "wig", drop = TRUE)