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This function is an easy-to-use wrapper for the multiple function calls necessary to enrich a given gene-list using Enrichr. see details section for more information.

Usage

rba_enrichr(
  gene_list,
  description = NULL,
  gene_set_library = "all",
  regex_library_name = TRUE,
  organism = "human",
  progress_bar = FALSE,
  ...
)

Arguments

gene_list

A vector with Entrez gene symbols.

description

(optional) A name or description to be associated with your uploaded gene-set to Enrichr servers.

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

This function will call other rba_enrichr_*** functions with the following order:

  1. (If neccessary) Call rba_enrichr_libs to obtain a list of available libraries in Enrichr.

  2. Call rba_enrichr_add_list to upload your gene-list and obtain a 'user list ID'.

  3. Call rba_enrichr_enrich to enrich the gene-list against one or multiple Enrichr libraries

Corresponding API Resources

"GET https://maayanlab.cloud/Enrichr/datasetStatistics"
"POST https://maayanlab.cloud/Enrichr/addList"
"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

# \donttest{
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"))
# }
# \donttest{
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"),
    gene_set_library = "GO_Molecular_Function_2017",
    regex_library_name = FALSE)
# }
# \donttest{
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"),
    gene_set_library = "go",
    regex_library_name = TRUE)
# }