import.gff: Import a GFF file

Description Usage Arguments Value Author(s)

Description

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.

Usage

1
  import.gff(file, row.pattern = NULL)

Arguments

file

the path to a gff file

row.pattern

currently unused

Value

a data.frame with these columns: "chr", "source", "feature", "start", "end", "score", "strand", "frame", "group"

Author(s)

Mark Cowley, 2/1/08


drmjc/genomics documentation built on May 15, 2019, 2:22 p.m.