Retrieve a core set of orthologs from pairwise ortholog tables — retrieve_core

Given an ortholog table generated with generate_ortholog_tables_all or a lncRNA map generated with map_generator_lnc, this function determines a core set of orthologs that are shared between all species.

Both table types are supported and detected automatically:

Protein-coding tables use species column subject_species and query column query_gene_locus_id.
lncRNA maps use species column species and query column query_id.

Usage

retrieve_core_orthologs(ortho_tables, species_order)

Arguments

ortho_tables: an ortholog table generated with generate_ortholog_tables_all or a lncRNA map generated with map_generator_lnc.
species_order: a character string specifying species names listed in the order of phylogenetic/taxonomic distance from the query species. The species names must match the species names present in ortho_tables.

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# Protein-coding ortholog table (subject_species + query_gene_locus_id)
ortho_tbl <- tibble::tibble(
  query_species       = "Arabidopsis_thaliana",
  subject_species     = rep(c("Arabidopsis_lyrata", "Brassica_rapa"), each = 3),
  query_id            = rep(c("AT1G01010.1", "AT1G01020.1", "AT1G01030.1"), 2),
  query_gene_locus_id = rep(c("AT1G01010", "AT1G01020", "AT1G01030"), 2),
  subject_id          = paste0("subj_", seq_len(6)),
  q_len               = rep(c(430L, 246L, 359L), 2),
  alig_length         = rep(c(430L, 246L, 355L), 2)
)
retrieve_core_orthologs(ortho_tbl,
                        species_order = c("Arabidopsis_lyrata", "Brassica_rapa"))

# lncRNA map (species + query_id) — column layout detected automatically
lnc_tbl <- tibble::tibble(
  species     = rep(c("Arabidopsis_lyrata", "Brassica_rapa"), each = 2),
  query_id    = rep(c("lnc001", "lnc002"), 2),
  subject_id  = paste0("slnc_", seq_len(4)),
  q_len       = rep(c(500L, 800L), 2),
  alig_length = rep(c(490L, 800L), 2)
)
retrieve_core_orthologs(lnc_tbl,
                        species_order = c("Arabidopsis_lyrata", "Brassica_rapa"))
                        } # }