Parse a GFF/GTF file as GRangesList of exons
parse_gtf(file, ...)path to a GFF or GTF file (See makeTxDbFromGFF))
other options passed to file path to makeTxDbFromGFF)
A GRangesList of exons grouped by transcripts
gff_file <- system.file("extdata","GFF3_files","a.gff3",package="splice2neo")
parse_gtf(gff_file)
#> Import genomic features from the file as a GRanges object ...
#> OK
#> Prepare the 'metadata' data frame ...
#> OK
#> Make the TxDb object ...
#> OK
#> GRangesList object of length 488:
#> $Solyc00g005000.2.1
#> GRanges object with 2 ranges and 3 metadata columns:
#> seqnames ranges strand | exon_id exon_name exon_rank
#> <Rle> <IRanges> <Rle> | <integer> <character> <integer>
#> [1] SL2.40ch00 16437-17275 + | 1 Solyc00g005000.2.1.1 1
#> [2] SL2.40ch00 17336-18189 + | 2 Solyc00g005000.2.1.2 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $Solyc00g005020.1.1
#> GRanges object with 3 ranges and 3 metadata columns:
#> seqnames ranges strand | exon_id exon_name exon_rank
#> <Rle> <IRanges> <Rle> | <integer> <character> <integer>
#> [1] SL2.40ch00 68062-68211 + | 3 Solyc00g005020.1.1.1 1
#> [2] SL2.40ch00 68344-68568 + | 4 Solyc00g005020.1.1.2 2
#> [3] SL2.40ch00 68654-68764 + | 5 Solyc00g005020.1.1.3 3
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $Solyc00g005040.2.1
#> GRanges object with 4 ranges and 3 metadata columns:
#> seqnames ranges strand | exon_id exon_name
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] SL2.40ch00 550920-550945 + | 6 Solyc00g005040.2.1.1
#> [2] SL2.40ch00 551034-551132 + | 7 Solyc00g005040.2.1.2
#> [3] SL2.40ch00 551218-551250 + | 8 Solyc00g005040.2.1.3
#> [4] SL2.40ch00 551343-551576 + | 9 Solyc00g005040.2.1.4
#> exon_rank
#> <integer>
#> [1] 1
#> [2] 2
#> [3] 3
#> [4] 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> ...
#> <485 more elements>