parse_gff_tree {FLAMES} | R Documentation |
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.
parse_gff_tree(gff_file)
gff_file |
the file path to the gff3 file to parse |
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.
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 = "/")))]] ## Not run: parsed_gff <- parse_gff_tree(gff) ## End(Not run)