Upload Your Gene-List to Enrichr

This function uploads your gene list to Enrichr and retrieves a unique 'user list ID' required for performing enrichment analysis.

Usage

rba_enrichr_add_list(
  gene_list,
  description = NULL,
  organism = "human",
  speedrichr = FALSE,
  ...
)

Arguments

gene_list: A character vector with Entrez gene symbols of test genes.
description: (optional) A description to be associated with your uploaded gene-set to Enrichr servers.
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).
speedrichr: logical (default = FALSE) Set to TRUE if you will use this gene list with a background list; otherwise, set to FALSE. Only available for human libraries. Refer to the details section for more information.
...: rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list with the unique IDs for your uploaded gene list. `userListId` is the ID required for later steps.

Details

Enrichr uses separate APIs for analysis with or without a background gene list. Set `speedrichr = TRUE` if this gene list will be used with a background gene list; otherwise, set it to FALSE. Gene lists submitted with `speedrichr = TRUE` can only be analyzed with a background set, and those submitted with `speedrichr = FALSE` can only be analyzed without one. Currently, background-based enrichment is supported only for human libraries.

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.

Corresponding API Resources

"POST https://maayanlab.cloud/Enrichr/addList"
"POST https://maayanlab.cloud/speedrichr/api/addList"

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

Examples

# \donttest{
rba_enrichr_add_list(gene_list = c("TP53", "TNF", "EGFR"),
     description = "tumoral genes",
     speedrichr = FALSE)
# }
# \donttest{
rba_enrichr_add_list(gene_list = c("RAG1", "RAG2", "DNTT", "LIG4", "ARTEMIS"),
     description = "TCR rearrangment",
     speedrichr = TRUE)
# }