gffToDataFrame {SynExtend} | R Documentation

## Generate a DataFrame of gene calls from a gff3 file

### Description

Generate a DataFrame of gene calls from a gff3 file

### Usage

    gffToDataFrame(GFF,
                   AdditionalAttrs = NULL,
                   AdditionalTypes = NULL,
                   RawTableOnly = FALSE,
                   Verbose = FALSE)

### Arguments

`GFF` | A url or filepath specifying a gff3 file to import
`AdditionalAttrs` | A vector of character strings to designate the attributes to pull. Default Attributes include: ”ID”, ”Parent”, ”Name”, ”gbkey”, ”gene”, ”product”, ”protein_id”, ”gene_biotype”, and ”Note”.
`AdditionalTypes` | A vector of character strings to query from the the ”Types” column. Default types are limited to ”Gene” and ”Pseudogene”, but any possible entry for ”Type” in a gff3 format can be added, such as ”rRNA”, or ”CRISPR_REPEAT”.
`RawTableOnly` | Logical specifying whether to return the raw imported GFF without complex parsing. Remains as a holdover from function construction and debugging. For simple gff3 import see `rtracklayer::import`.
`Verbose` | Logical specifying whether to print a progress bar and time difference.

### Details

Import a gff file into a rectangular parsable object.

### Value

A DataFrame with relevant information extracted from a GFF.

### Author(s)

Nicholas Cooley npc19@pitt.edu

### Examples

    ImportedGFF <- gffToDataFrame(GFF = system.file("extdata",
                                                    "GCA_006740685.1_ASM674068v1_genomic.gff.gz",
                                                    package = "SynExtend"),
                                  Verbose = TRUE)

[Package SynExtend version 1.0.0 Index]