rba_enrichr_add_background: Upload Background Gene-List to Enrichr

In rbioapi: User-Friendly R Interface to Biologic Web Services' API

Upload Background Gene-List to Enrichr

Description

In addition to the main gene list, you can also submit a background gene list to Enrichr. This gene list can be used later to compute the statistics of the enrichment analysis.

Usage

rba_enrichr_add_background(background_genes, ...)

Arguments

background_genes	A character vector of Entrez gene symbols of the background genes.
...	rbioapi option(s). See rba_options's arguments manual for more information on available options.

Details

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.

Value

A list with the unique IDs for your uploaded background gene list.

Corresponding API Resources

"POST https://maayanlab.cloud/speedrichr/api/addbackground"

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_list(), rba_enrichr_enrich(), rba_enrichr_gene_map(), rba_enrichr_libs(), rba_enrichr_view_list()

Examples

my_background_genes <- c(
"NSUN3", "POLRMT", "NLRX1", "SFXN5", "ZC3H12C", "SLC25A39", "ARSG",
"DEFB29", "PCMTD2", "ACAA1A", "LRRC1", "2810432D09RIK", "SEPHS2",
"SAC3D1", "TMLHE", "LOC623451", "TSR2", "PLEKHA7", "GYS2", "ARHGEF12",
"HIBCH", "LYRM2", "ZBTB44", "ENTPD5", "RAB11FIP2", "LIPT1",
"INTU", "ANXA13", "KLF12", "SAT2", "GAL3ST2", "VAMP8", "FKBPL",
"AQP11", "TRAP1", "PMPCB", "TM7SF3", "RBM39", "BRI3", "KDR", "ZFP748",
"NAP1L1", "DHRS1", "LRRC56", "WDR20A", "STXBP2", "KLF1", "UFC1",
"CCDC16", "9230114K14RIK", "RWDD3", "2610528K11RIK")

rba_enrichr_add_background(background_genes = my_background_genes)

rbioapi documentation built on April 4, 2025, 5:04 a.m.