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Parse Gff3 file

Source: R/parse_gene_anno.R
parse_gff_tree.Rd

Parse a Gff3 file into 3 components: chromasome to gene name, a transcript dictionary, a gene to transcript dictionary and a transcript to exon dictionary. These components are returned in a named list.

Usage

parse_gff_tree(gff_file)

Arguments

gff_file

the file path to the gff3 file to parse

Value

a named list with the elements "chr_to_gene", "transcript_dict", "gene_to_transcript", "transcript_to_exon", containing the data parsed from the gff3 file.

Examples

temp_path <- tempfile()
bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE)
file_url <-
    "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data"
gff <- bfc[[names(BiocFileCache::bfcadd(bfc, "GFF", paste(file_url, "SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf", sep = "/")))]]
if (FALSE) parsed_gff <- parse_gff_tree(gff) # \dontrun{}