rba_panther_ortholog {rbioapi}

Search PANTHER for Orthologs of Gene(s)

Description

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 vector of genes identifiers with maximum length of 10 or only one if seq_pos is supplied. Can be any of: Ensemble gene ID, Ensemble protein ID, Ensemble 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

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

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

Examples

rba_panther_ortholog("CD40", organism = 9606, type = "LDO")