Description Usage Arguments Value Author(s)
from:
http://genome.ucsc.edu/FAQ/FAQformat#format3
GFF
(General Feature Format) lines are based on the GFF
standard file format. GFF lines have nine required fields
that must be tab-separated. If the fields are separated
by spaces instead of tabs, the track will not display
correctly. For more information on GFF format, refer to
http://www.sanger.ac.uk/Software/formats/GFF. Here
is a brief description of the GFF fields:
seqname -
The name of the sequence. Must be a chromosome or
scaffold.
source - The program that generated this
feature.
feature - The name of this type of feature.
Some examples of standard
feature types are "CDS",
"start_codon", "stop_codon", and "exon".
start - The
starting position of the feature in the sequence. The
first base is numbered 1.
end - The ending position of
the feature (inclusive).
score - A score between 0 and
1000. If the track line useScore attribute is set to 1
for this annotation data set, the score value will
determine the level of gray in which this feature is
displayed (higher numbers = darker gray). If there is no
score value, enter ".".
strand - Valid entries include
'+', '-', or '.' (for don't know/don't care).
frame -
If the feature is a coding exon, frame should be a number
between 0-2 that represents the reading frame of the
first base. If the feature is not a coding exon, the
value should be '.'.
group - All lines with the same
group are linked together into a single item.
1 | import.gff(file, row.pattern = NULL)
|
file |
the path to a gff file |
row.pattern |
currently unused |
a data.frame
with these columns: "chr", "source",
"feature", "start", "end", "score", "strand", "frame",
"group"
Mark Cowley, 2/1/08
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