parse_gff_tree {FLAMES} | R Documentation

## Parse Gff3 file

### Description

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 = "/")))]]
    ## Not run:
    parsed_gff <- parse_gff_tree(gff)

    ## End(Not run)

[Package FLAMES version 1.0.2 Index]