rbioapi (version 0.8.2)

rba_enrichr_add_background: 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, ...)

Value

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

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.

Corresponding API Resources

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

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.

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

# \donttest{
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)
# }