rbioapi: rba_reactome_analysis_species – R documentation

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rba_reactome_analysis_species

Compare Human Pathways with with Other Species

Description

Use This function to Compare human's manually-curated pathways and computationally inferred pathways (orthologous) in other species.

Usage

rba_reactome_analysis_species(
  species_dbid,
  sort_by = "ENTITIES_PVALUE",
  order = "ASC",
  resource = "TOTAL",
  p_value = 1,
  min = NA,
  max = NA,
  ...
)

Arguments

`species_dbid`	Numeric: Reactome DbId (e.g Mus musculus is 48892) of the species you want to compare with Homo sapiens. Refer to `rba_reactome_species` or Reactome Data Schema: Entries: Species.
`sort_by`	Sort the result based on what column? available choices are: "NAME", "TOTAL_ENTITIES", "TOTAL_INTERACTORS", "TOTAL_REACTIONS", "FOUND_ENTITIES", "FOUND_INTERACTORS", "FOUND_REACTIONS", "ENTITIES_RATIO", "ENTITIES_PVALUE", "ENTITIES_FDR" or "REACTIONS_RATIO"
`order`	Sort Order. Can be either "ASC" (default) or "DESC".
`resource`	Filter results based on the resource. Default is "TOTAL", available choices are: "TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND", "ENTITIES_FDR" or "PUBCHEM_COMPOUND".
`p_value`	Set a P value threshold. Only results with P value equal to or less than your provided threshold will be returned. (default = 1, Meaning no P value filtering)
`min`	(numeric) Minimum number of entities that a pathways should have to be included in the results.
`max`	(numeric) Maximum number of entities that a pathways should have to be included in the results.
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

Details

Reactome incorporate manually curated human reactions and PANTHER's protein homology data to Computationally infer events in other eukaryotic species.
In version 73 (11 June 2020), using an orthology-based approach, Homo sapiens events was projected to 18,654 orthologous pathways (with 81,835 orthologous proteins) in 15 non-human species. Refer to Reactome Computationally Inferred Events for more information.

Value

List with the results of the comparison.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/species/homoSapiens/species"

References

Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H. Reactome pathway analysis: a high-performance in-memory approach. BMC bioinformatics. 2017 Mar;18(1) 142. doi: 10.1186/s12859-017-1559-2. PubMed PMID: 28249561. PubMed Central PMCID: PMC5333408.
Reactome Analysis Services API Documentation

Examples

rba_reactome_analysis_species(species_dbid = 48892)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release