gffToDataFrame {SynExtend} | R Documentation |
Generate a DataFrame of gene calls from a gff3 file
gffToDataFrame(GFF, AdditionalAttrs = NULL, AdditionalTypes = NULL, RawTableOnly = FALSE, Verbose = FALSE)
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 |
Verbose |
Logical specifying whether to print a progress bar and time difference. |
Import a gff file into a rectangular parsable object.
A DataFrame with relevant information extracted from a GFF.
Nicholas Cooley npc19@pitt.edu
ImportedGFF <- gffToDataFrame(GFF = system.file("extdata", "GCA_006740685.1_ASM674068v1_genomic.gff.gz", package = "SynExtend"), Verbose = TRUE)