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A One-step Wrapper for miRNA Enrichment Using miEAA

Source: R/mieaa.R
rba_mieaa_enrich.Rd

This function is a wrapper for the multiple function calls necessary to perform enrichment analysis on a given miRNA list using miEAA. See Details section for more information.

Usage

rba_mieaa_enrich(
  test_set,
  mirna_type,
  test_type,
  species,
  categories = NULL,
  p_adj_method = "fdr",
  independent_p_adj = TRUE,
  sig_level = 0.05,
  min_hits = 2,
  ref_set = NULL,
  sort_by = "p_adjusted",
  sort_asc = TRUE,
  poll_interval = 5,
  poll_timeout = 300,
  ...
)

Arguments

test_set

Character vector: Mature or precursor miRBase miRNA identifiers. Note that

  1. Only miRBase v22 identifiers are accepted. You can use rba_mieaa_convert_version to convert older identifiers to miRBase v22.

  2. The list must contain either mature or precursor miRNA identifiers, not a mixture of both.

mirna_type

Character: Type of the supplied miRNA identifiers; either "mature" or "precursor".

test_type

Character: Analysis to perform; either "ORA" for over-representation analysis or "GSEA" for miRNA gene set enrichment analysis. For GSEA, the input list must already be ranked by an appropriate criterion.

species

Character or Numeric: Scientific name, abbreviation, or NCBI taxon ID of one of the following species:

  1. "Homo sapiens", "hsa" or 9606

  2. "Mus musculus", "mmu" or 10090

  3. "Rattus norvegicus", "rno" or 10116

  4. "Arabidopsis thaliana", "ath" or 3702

  5. "Bos taurus", "bta" or 9913

  6. "Caenorhabditis elegans", "cel" or 6239

  7. "Drosophila melanogaster", "dme" or 7227

  8. "Danio rerio", "dre" or 7955

  9. "Gallus gallus", "gga" or 9031

  10. "Sus scrofa", "ssc" or 9823

categories

Character vector: (default = NULL) One or more category identifiers to use for miRNA set enrichment analysis. Note that

  • Available categories vary with the selected species and whether the supplied miRNAs are mature or precursor. Use rba_mieaa_cats to retrieve a list of available category identifiers for a given species and miRNA type.

  • If NULL, the analysis is performed using all available categories.

p_adj_method

Character: (default = "fdr") P-value adjustment method to use. One of: "none", "fdr", "bonferroni", "BY", "hochberg", "holm", or "hommel".

independent_p_adj

Logical: (default = TRUE) The scope of p-value adjustment. If TRUE, p-values are adjusted separately within each category. If FALSE, p-values are adjusted collectively over all categories.

sig_level

Numeric: (default = 0.05) Significance threshold for adjusted p-values. Values equal to or greater than this threshold are omitted from the results. Must be greater than 0 and at most 1.

min_hits

Numeric: (default = 2) Minimum number of miRNAs from the test set that a subcategory must contain to be included in the results. Must be a positive integer.

ref_set

Character vector: (default = NULL) Only applicable when test_type = "ORA". Used as the reference (background or universe) set for p-value calculations.

sort_by

Character: (default = "p_adjusted") Result column to sort by. One of: "category", "subcategory", "enrichment", "p_value", "p_adjusted", "q_value", or "observed".

sort_asc

Logical: (default = TRUE) If TRUE, sort the results in ascending order. If FALSE, sort them in descending order.

poll_interval

Numeric: (default = 5) Number of seconds to wait between job-status requests; must be between 5 and 300 seconds.

poll_timeout

Numeric: (default = 300) Maximum number of seconds to wait for the enrichment analysis to finish. Use Inf to wait without a time limit.

...

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

Value

A data frame with your enrichment analysis results.

Details

This function will call other rba_mieaa_*** functions with the following order:

  1. Call rba_mieaa_enrich_submit to submit an enrichment analysis request to the miEAA server using the supplied miRNA list and other arguments.

  2. Once the job is successfully submitted, call rba_mieaa_enrich_status at the selected polling interval to check whether the server-side analysis has finished.

  3. Call rba_mieaa_enrich_results to retrieve the results of your enrichment analysis.

See each function's manual for more details. The save_file rbioapi option applies only to the final enrichment results and not to the intermediate submission or status responses.

Corresponding API Resources

"https://ccb-compute2.cs.uni-saarland.de/mieaa/api/"

References

  • Ernesto Aparicio-Puerta, Pascal Hirsch, Georges P. Schmartz, Fabian Kern, Tobias Fehlmann, Andreas Keller, miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations, Nucleic Acids Research, Volume 51, Issue W1, 5 July 2023, Pages W319–W325, https://doi.org/10.1093/nar/gkad392

  • miEAA browsable API tutorial

  • Citation note on miEAA website

See also

Other "miEAA": rba_mieaa_cats(), rba_mieaa_convert_type(), rba_mieaa_convert_version(), rba_mieaa_enrich_results(), rba_mieaa_enrich_status(), rba_mieaa_enrich_submit()

Other "Enrichment/Over-representation": rba_enrichr(), rba_panther_enrich(), rba_reactome_analysis(), rba_string_enrichment(), rba_string_enrichment_image()

Examples

if (FALSE) { # \dontrun{
rba_mieaa_enrich(test_set = c("hsa-miR-20b-5p", "hsa-miR-144-5p",
 "hsa-miR-17-5p", "hsa-miR-20a-5p"),
     mirna_type = "mature",
     test_type = "ORA",
     species = 9606,
     categories = "miRPathDB_GO_Biological_process_mature")
} # }