gffToDataFrame: Generate a DataFrame of gene calls from a gff3 file

In SynExtend: Tools for Working With Synteny Objects

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 [e-mail]

Examples

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

SynExtend documentation built on Nov. 8, 2020, 7:50 p.m.