rba_enrichr_add_background {rbioapi} | R Documentation |
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 |
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
See Also
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)