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

Examples

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