rba_mieaa_enrich {rbioapi}

A One-step Wrapper for miRNA Enrichment Using miEAA

Description

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,
  ...
)

Arguments

test_set

a character vector with your mature or precursor miRBase miRNA accessions. Note that

1. Only miRBase v22 miRNA accession are accepted. You can use rba_mieaa_convert_version to convert your accessions to miRBase v22.

2. Your list should be entirely consisted of either mature or precursor miRNA accession. A mixture of both is not accepted.

mirna_type

Type of your supplied miRNA accession. either "mature" or "precursor".

test_type

The analysis to perform. can be either "ORA" for 'Over Representation Analysis' or "GSEA" for miRNA (Gene) 'Set Enrichment Analysis'. Note that in GSEA, your list should be sorted beforehand based on some criterion.

species

Fully or partially matching 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

one or multiple Category names to be used for miRNA set enrichment analysis. Note that

• Available categories varies based on your chosen specie and if your supplied miRNA type is mature or precursor. Use rba_mieaa_cats to retrieve a list of available category names for a given specie and miRNA type.

• If you supply NULL, the analysis will be performed on all of the available categories.

p_adj_method

P-value adjustment method to be used. Should be one of: "none", "fdr" (default), "bonferroni", "BY", "hochberg", "holm" or "hommel"

independent_p_adj

(logical) The scope and level of p-value adjustment; if TRUE (default), the categories will be considered independent from each other and the p-value will be adjusted separately for each category. if FALSE, the p-value will be adjusted collectively over all categories.

sig_level

(numeric) The significance threshold of adjusted P-value. values equal to or greater than this threshold will be dropped from the results.

min_hits

(numeric) How many miRNA should a sub-category have from your supplied test-list to be included in the results? (default is 2)

ref_set

(Optional) Only applicable when test_type is "ORA". This character vector will be used as your reference (background or universe) set for p-value calculations.

sort_by

A column name to the result's table based on that. one of: "category", "subcategory", "enrichment", "p_value", "p_adjusted" (default), "q_value" or "observed" .

sort_asc

(logical) If TRUE, the results will be sorted in ascending order. If FALSE, the results will be sorted in descending order.

...

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

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 miEAA servers, using your supplied miRNA lists and other arguments.

2. Once your job was successfully submitted, it will call rba_mieaa_enrich_status every 5 seconds, to check the status of your running server-side job and whether your analysis job is finished and the results are available.

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

See each function's manual for more details.

Value

A data frame with your enrichment analysis results.

Corresponding API Resources

"GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/"

References

• Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig,Eckart Meese, Andreas Keller, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W521–W528, https://doi.org/10.1093/nar/gkaa309

• miEAA browsable API tutorial

• Citations 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()

Examples

## Not run: 
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")

## End(Not run)