rba_enrichr_enrich {rbioapi} | R Documentation |
Get Enrichr Enrichment Results
Description
This function retrieves enrichment analysis results for your supplied 'user_list_id' against one or multiple Enrichr libraries.
Usage
rba_enrichr_enrich(
user_list_id,
gene_set_library = "all",
regex_library_name = TRUE,
organism = "human",
background_id = NULL,
progress_bar = TRUE,
...
)
Arguments
user_list_id |
An ID returned after uploading a gene list
using |
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). If 'background_id' is provided, the only available option is "human". |
background_id |
An ID returned after uploading a background gene
list using |
progress_bar |
logical: (default = TRUE) if multiple Enrichr libraries are selected, should a progress bar be displayed? |
... |
rbioapi option(s). See |
Details
If 'background_id' is supplied, this function will interact with the
speedrichr API. In this case, 'user_list_id' must have been obtained
from a rba_enrichr_add_list
call with the 'speedrichr'
parameter set to 'TRUE'. Additionally, this feature is only available
for "human" organism.
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 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/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()
,
rba_enrichr_add_background()
,
rba_enrichr_add_list()
,
rba_enrichr_gene_map()
,
rba_enrichr_libs()
,
rba_enrichr_view_list()
Examples
## Not run:
rba_enrichr_enrich(user_list_id = 11111)
## End(Not run)
## Not run:
rba_enrichr_enrich(user_list_id = 11111,
gene_set_library = "GO_Molecular_Function_2017",
regex_library_name = FALSE)
## End(Not run)
## Not run:
rba_enrichr_enrich(user_list_id = 11111,
gene_set_library = "go",
regex_library_name = TRUE)
## End(Not run)