| readGff3 {genomeIntervals} | R Documentation |
Make a Genome_intervals_stranded object from a gff file in gff3 format.
readGff3(file, isRightOpen=TRUE)
file |
The name of the gff file to read. |
isRightOpen |
Although a proper GFF3 file follows the convention of right-open intervals,
improper GFF files following the right-closed convention are frequently found.
Set isRightOpen = FALSE in this case.
|
The file must follow gff3 format specifications as in
http://www.sequenceontology.org/gff3.shtml. The file is read as a
table. Meta-information (lines starting with ###) are not parsed. A
“.” in, for example, the gff file's score or
frame field will be converted to NA.
When the GFF file follows the right-open interval convention (isRightOpen is TRUE), then
GFF entries for which end base equals first base are recognized as zero-length features
and loaded as inter_base intervals.
A Genome_intervals_stranded object image of the
gff file. The GFF3 fields seqid, source, type, score, strand, phase and
attributes are stored in the annotation slot and renamed as seq_name, source,
type, score, strand, phase and gffAttributes respectively.
Potential FASTA entries at the end of the file are ignored.
The functions getGffAttribute and parseGffAttributes for parsing GFF attributes.
# Get file path
libPath <- installed.packages()["genomeIntervals", "LibPath"]
filePath <- file.path(
libPath,
"genomeIntervals",
"example_files"
)
# Load SGD gff
# SGD does not comply to the GFF3 right-open interval convention
gff <- readGff3( file.path( filePath, "sgd_simple.gff"), isRightOpen = FALSE)
head(gff,10)
head(annotation(gff),10)