Select best splice variant representing orthologous gene loci

This function selects orthologs based on either gene locus or splice variant.

select_best_splice_variants(
  dnds_tbl,
  annotation_file_query,
  annotation_file_subject,
  collapse_by = "gene_locus",
  format = c("gtf", "gtf")
)

Arguments

dnds_tbl	a tibble returned by dnds.
annotation_file_query	file path to query annotation file in either gtf or gff format.
annotation_file_subject	file path to query annotation file in either gtf or gff format.
collapse_by	locus type by which orthologs should be determined. Options are: type = "gene_locus": the splice variant having the lowest e-value of the BLAST search is chosen to represent the gene locus for the orthology relationship. type = "splice_variant": all splice variants of homologous gene loci will be returned.
format	a vector of length 2 storing the annotation file formats of the query annotation file and subject annotation file: either gtf or gff format. E.g. format = c("gtf","gtf").

See also

dnds, internal_import_dnds_across_multiple_species, import_dnds_across_multiple_species, dnds_across_multiple_species

Author

Hajk-Georg Drost