import.gff {rtracklayer} | R Documentation |
These are the functions for importing trackSet
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 trackSet
or one of its subclasses,
except for import.ucsc
, which returns a
trackSets
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)