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)