Submit miEAA miRNA Enrichment Analysis Request

Submit a request to the miEAA server to perform over-representation analysis or gene set enrichment analysis for a set of miRNA identifiers.

Usage

rba_mieaa_enrich_submit(
  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,
  ...
)

Arguments

test_set

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

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

"Homo sapiens", "hsa" or 9606
"Mus musculus", "mmu" or 10090
"Rattus norvegicus", "rno" or 10116
"Arabidopsis thaliana", "ath" or 3702
"Bos taurus", "bta" or 9913
"Caenorhabditis elegans", "cel" or 6239
"Drosophila melanogaster", "dme" or 7227
"Danio rerio", "dre" or 7955
"Gallus gallus", "gga" or 9031
"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.

...

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

Value

A list that contains your submitted job's ID and a URL to manually check for your job status.

Details

Note that using rba_mieaa_enrich is a more convenient way to automatically perform this and other required function calls to perform enrichment analysis on your input miRNA-set using miEAA.

Corresponding API Resources

"POST https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_analysis/{species}/{type}/{test}/"

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

Examples

# \donttest{
Sys.sleep(1) # to prevent 429 error during R CMD check
rba_mieaa_enrich_submit(test_set = c("hsa-miR-20b-5p", "hsa-miR-144-5p"),
    mirna_type = "mature",
    test_type = "GSEA",
    species = 9606,
    categories = NULL)
# }