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This function which will retrieve the enrichment results of your supplied gene-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",
  progress_bar = TRUE,
  ...
)

Arguments

user_list_id

An ID returned to you after uploading a gene list using rba_enrichr_add_list

gene_set_library

One of the:

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

  2. A gene-set library name existed in the results retrieved via 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 regarded as a regex or partially matching name. if FALSE, gene_set_library will be considered 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).

progress_bar

logical: In case of selecting multiple Enrichr libraries, should a progress bar be displayed?

...

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

Value

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

Details

Note that using rba_enrichr is a more convenient way to automatically perform this and other required function calls to enrich your input gene-set.

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/enrich"

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: https://doi.org/10.1002/cpz1.90

  • Enrichr API Documentation

  • Citations note on Enrichr website

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)
}