load_trinotate_go: Read a csv file from trinotate and extract ontology data from...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Read a csv file from trinotate and extract ontology data from it.

Description

Trinotate performs some neat sequence searches in order to seek out likely annotations for the trinity contigs. This function extracts ontology data from it. Keep in mind that this data is primarily from Blast2GO.

Usage

load_trinotate_go(
  trinotate = "reference/trinotate.csv",
  blast2go_column = "gene_ontology_BLASTX",
  pfam_column = "gene_ontology_Pfam",
  length_column = "transcript",
  fill = 1500,
  collapse = TRUE,
  id_column = "#gene_id"
)

Arguments

trinotate	CSV of trinotate annotation data.
blast2go_column	Column name containing BLAST2GO data.
pfam_column	Column containing data from pfam searches.
length_column	Column containing the gene lengths.
fill	Cheat and fill in an arbitrary value for gene lengths if all else fails.
collapse	Collapse isforms to genes?
id_column	Column containing the gene IDs.

Value

List of the extracted GO data, a table of it, length data, and the resulting length table.

See Also

[load_trinotate_annotations()]

Examples

 sb_annot <- get_sbetaceum_data()[["annot"]]
 trinotate_go <- load_trinotate_go(trinotate = sb_annot)
 dim(trinotate_go$go_data)
 dim(trinotate_go$go_table)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.