rba_enrichr {rbioapi} | R Documentation |
A One-step Wrapper for Gene-list Enrichment Using Enrichr
Description
This function provides a convenient one-step wrapper for performing enrichment analysis on a given gene list using Enrichr. It simplifies the process by internally calling the necessary functions in the correct order. See the details section for more information.
Usage
rba_enrichr(
gene_list,
description = NULL,
gene_set_library = "all",
regex_library_name = TRUE,
organism = "human",
background_genes = NULL,
progress_bar = TRUE,
...
)
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. |
gene_set_library |
One of the:
|
regex_library_name |
logical: if TRUE (default) the supplied gene_set_library will be considered as a regex pattern. If FALSE, gene_set_library will be considered as an 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). |
background_genes |
A character vector of Entrez gene symbols of the background genes. |
progress_bar |
logical: (default = TRUE) if multiple Enrichr libraries are selected, should a progress bar be displayed? |
... |
rbioapi option(s). See |
Details
This function will call other rba_enrichr_*** functions with the following order:
(If necessary) Call
rba_enrichr_libs
to obtain a list of available libraries in Enrichr for the given organism.Call
rba_enrichr_add_list
to upload your gene-list and obtain a 'user list ID'.(If necessary) Call
rba_enrichr_add_background
to upload your background gene-list and obtain a 'background list ID'.Call
rba_enrichr_enrich
to perform enrichment analysis on the gene-list against one or multiple Enrichr libraries
Value
A list containing data frames of the enrichment results of your supplied gene-list against the selected Enrichr libraries.
Corresponding API Resources
"GET https://maayanlab.cloud/Enrichr/datasetStatistics"
"POST https://maayanlab.cloud/Enrichr/addList"
"POST https://maayanlab.cloud/speedrichr/api/addList"
"POST https://maayanlab.cloud/speedrichr/api/addbackground"
"GET https://maayanlab.cloud/Enrichr/enrich"
"POST https://maayanlab.cloud/speedrichr/api/backgroundenrich"
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_add_background()
,
rba_enrichr_add_list()
,
rba_enrichr_enrich()
,
rba_enrichr_gene_map()
,
rba_enrichr_libs()
,
rba_enrichr_view_list()
Other "Enrichment/Over-representation":
rba_mieaa_enrich()
,
rba_panther_enrich()
,
rba_reactome_analysis()
,
rba_string_enrichment()
,
rba_string_enrichment_image()
Examples
## Not run:
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"))
## End(Not run)
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"),
gene_set_library = "GO_Molecular_Function_2017",
regex_library_name = FALSE)
rba_enrichr(gene_list = c("TP53", "TNF", "EGFR"),
gene_set_library = "go",
regex_library_name = TRUE)