rba_enrichr {rbioapi} | R Documentation |
A One-step Wrapper for Gene-list Enrichment Using Enrichr
Description
This function is an easy-to-use wrapper for the multiple function calls necessary to perform enrichment analysis on a given gene-list using Enrichr. see details section for more information.
Usage
rba_enrichr(
gene_list,
description = NULL,
gene_set_library = "all",
regex_library_name = TRUE,
organism = "human",
progress_bar = FALSE,
...
)
Arguments
gene_list |
A vector with Entrez gene symbols. |
description |
(optional) A name or 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 regarded as a regex or partially matching name. if FALSE, gene_set_library will be considered 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). |
progress_bar |
logical: In case of selecting multiple Enrichr libraries, should a progress bar be displayed? |
... |
rbioapi option(s). See |
Details
This function will call other rba_enrichr_*** functions with the following order:
(If neccessary) Call
rba_enrichr_libs
to obtain a list of available libraries in Enrichr.Call
rba_enrichr_add_list
to upload your gene-list and obtain a 'user 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"
"GET https://maayanlab.cloud/Enrichr/enrich"
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_list()
,
rba_enrichr_enrich()
,
rba_enrichr_gene_map()
,
rba_enrichr_libs()
,
rba_enrichr_view_list()
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)