Using This function you can submit a request in miEAA servers to perform Over-representation or GSEA Analysis for a given set of miRNA identifiers. see "arguments" section for more information.
rba_mieaa_enrich_submit( test_set, mirna_type, test_type, species = "hsa", categories = NULL, p_adj_method = "fdr", independent_p_adj = TRUE, sig_level = 0.05, min_hits = 2, ref_set = NULL, ... )
a character vector with your mature or precursor miRBase miRNA accessions. Note that
Type of your supplied miRNA accession. either "mature" or "precursor".
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.
Fully or partially matching Scientific name, abbreviation or NCBI taxon ID of one of the following species:
one or multiple Category names to be used for miRNA set enrichment analysis. Note that
P-value adjustment method to be used. Should be one of: "none", "fdr" (default), "bonferroni", "BY", "hochberg", "holm" or "hommel"
(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.
(numeric) The significance threshold of adjusted P-value. values equal to or greater than this threshold will be dropped from the results.
(numeric) How many miRNA should a sub-category have from your supplied test-list to be included in the results? (default is 2)
(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.
rbioapi option(s). See
A list that contains your submitted job's ID and a URL to manually check for your job status.
Note that using
rba_mieaa_enrich is a more convenient way to
automatically perform this and other required function calls to enrich
your input miRNA-set using miEAA.
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