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Search PANTHER for Orthologs of Gene(s)

Source: R/panther.R
rba_panther_ortholog.Rd

Using this function you can search and retrieve orthologs of given gene(s), and optionally return the corresponding position in the target organisms' protein sequences.

Usage

rba_panther_ortholog(
  genes,
  organism,
  type = "all",
  target_organisms = NULL,
  seq_pos = NULL,
  include_msa = NULL,
  ...
)

Arguments

genes

Character or numeric vector of gene identifiers with maximum length of 10, or only one if seq_pos is supplied. Can be any of: Ensembl gene ID, Ensembl protein ID, Ensembl transcript ID, Entrez gene ID, gene symbol, NCBI GI, HGNC ID, International protein index ID, NCBI UniGene ID, UniProt accession and/or UniProt ID.

organism

(numeric) NCBI taxon ID of the organism of your supplied genes. run rba_panther_info with argument 'what = "organisms"' to get a list of PANTHER's supported organisms.

type

Ortholog types to return. either "all" (default) or "LDO" to only return least diverged orthologs.

target_organisms

(numeric) NCBI taxon ID(s) to filter the results. run rba_panther_info with argument 'what = "organisms"' to get a list of PANTHER's supported organisms.

seq_pos

(Numeric) A position in the protein's sequence of the supplied gene. should be in the range of the protein's length.

include_msa

(Logical) Only if a sequence position is supplied, should MSA (Multiple Sequence Alignment) information be included in the results?

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A data frame with Orthologs information.

Corresponding API Resources

"POST https://www.pantherdb.org/services/oai/pantherdb/ortholog/matchortho"
"POST https://www.pantherdb.org/services/oai/pantherdb/ortholog/homologpos"

References

See also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_genome(), rba_panther_homolog(), rba_panther_info(), rba_panther_mapping(), rba_panther_tree_grafter()

Examples

# \donttest{
rba_panther_ortholog("CD40", organism = 9606, type = "LDO")
# }