Select orthologs based on either gene locus or splice variant

Source: R/select_orthologs.R

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

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

Arguments

dnds_tbl

a tibble returned by link{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").

Author

Hajk-Georg Drost