Extract 5'UTR ranges from GFF or GTF — extract

Extract 5'UTR ranges from GFF or GTF.

Usage

extract_utr5(gff_file, format = "auto", utr5_info = "all")

Arguments

gff_file: Genomic structural annotation GFF3/GTF file path.
format: Format of GFF3/GTF file. ("auto", "gff3", "gtf").
utr5_info: mRNA information. ("all", "chrom_id", "utr5_id", "utr5_range").

Value

A GRanges object.

Author

benben-miao

Examples

# Example GFF3 file in GAnnoViz
gff_file <- system.file(
  "extdata",
  "example.gff3.gz",
  package = "GAnnoViz")

# Extract 5'UTR
utr5 <- extract_utr5(
  gff_file = gff_file,
  format = "auto",
  utr5_info = "all")
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK
utr5
#> GRanges object with 0 ranges and 3 metadata columns:
#>    seqnames    ranges strand |   exon_id   exon_name exon_rank
#>       <Rle> <IRanges>  <Rle> | <integer> <character> <integer>
#>   -------
#>   seqinfo: 22 sequences (1 circular) from an unspecified genome; no seqlengths

# 5'UTR info: utr5_range
utr5_range <- extract_utr5(
  gff_file = gff_file,
  format = "auto",
  utr5_info = "utr5_range")
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK
head(utr5_range)
#> IRanges object with 0 ranges and 0 metadata columns:
#>        start       end     width
#>    <integer> <integer> <integer>