rbioapi (version 0.8.2)

rba_enrichr_enrich: Get Enrichr Enrichment Results

Description

This function retrieves enrichment analysis results for your supplied `user_list_id` against one or multiple Enrichr libraries.

Usage

rba_enrichr_enrich(
  user_list_id,
  gene_set_library = "all",
  regex_library_name = TRUE,
  organism = "human",
  background_id = NULL,
  progress_bar = TRUE,
  ...
)

Value

A list containing data frames of the enrichment results of your supplied gene-list against the selected Enrichr libraries.

Arguments

user_list_id

An ID returned after uploading a gene list using rba_enrichr_add_list, with the `speedrichr` set to TRUE or FALSE depending on whether you intend to analyze this gene list with or without a background gene list, respectively.

gene_set_library

One of the:

1. "all" to select all of the available Enrichr gene-set libraries.

2. A gene-set library name. You can retrieve the available options for a given species using rba_enrichr_libs.

3. If regex_library_name = TRUE, A partially-matching name a regex pattern that correspond to one or more of Enrichr library names.

regex_library_name

logical: if TRUE (default) the supplied gene_set_library will be considered as a regex pattern. If FALSE, gene_set_library will be considered as an exact match.

organism

(default = "human") Which model organism version of Enrichr to use? Available options are: "human", (H. sapiens & M. musculus), "fly" (D. melanogaster), "yeast" (S. cerevisiae), "worm" (C. elegans) and "fish" (D. rerio). If `background_id` is provided, the only available option is "human".

background_id

An ID returned after uploading a background gene list using rba_enrichr_add_background

progress_bar

logical: (default = TRUE) if multiple Enrichr libraries are selected, should a progress bar be displayed?

...

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

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/enrich"
"POST https://maayanlab.cloud/speedrichr/api/backgroundenrich"

Details

If `background_id` is supplied, this function will interact with the speedrichr API. In this case, `user_list_id` must have been obtained from a rba_enrichr_add_list call with the `speedrichr` parameter set to `TRUE`. Additionally, this feature is only available for "human" organism.

Please note that rba_enrichr provides a one-step and more convenient way to automatically handle this and other required function calls needed to perform gene set enrichment analysis with Enrichr.

References

• Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

• Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma’ayan, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Research, Volume 44, Issue W1, 8 July 2016, Pages W90–W97, https://doi.org/10.1093/nar/gkw377

• Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., Jeon, M., & Ma’ayan, A. (2021). Gene set knowledge discovery with Enrichr. Current Protocols, 1, e90. doi: 10.1002/cpz1.90

• Enrichr API Documentation

• Citations note on Enrichr website

See Also

rba_enrichr

Other "Enrichr": rba_enrichr(), rba_enrichr_add_background(), rba_enrichr_add_list(), rba_enrichr_gene_map(), rba_enrichr_libs(), rba_enrichr_view_list()

Examples

if (FALSE) {
rba_enrichr_enrich(user_list_id = 11111)
}
if (FALSE) {
rba_enrichr_enrich(user_list_id = 11111,
    gene_set_library = "GO_Molecular_Function_2017",
    regex_library_name = FALSE)
}
if (FALSE) {
rba_enrichr_enrich(user_list_id = 11111,
    gene_set_library = "go",
    regex_library_name = TRUE)
}