enrichr | R Documentation |
Gene enrichment using Enrichr
enrichr(
genes,
databases = NULL,
background = NULL,
include_overlap = FALSE,
sleepTime = 1
)
genes |
(Required). Character vector of Entrez gene symbols as input. A data.frame of gene symbols in first column is also acceptable, optionally a score denoting the degree of membership between 0 and 1 in the second column. |
databases |
(Required). Character vector of databases to search. See https://maayanlab.cloud/Enrichr/ for available databases. |
background |
(Optional). Character vector of Entrez gene symbols to be used as
background. A data.frame of gene symbols in first column is also acceptable.
Default is |
include_overlap |
(Optional). Download database in GMT format to include 'Overlap'
in the resulting data.frame when analysing with a background. Default is |
sleepTime |
(Optional) Time to wait (in seconds) between sending requests to the server to prevent the same results being returned as the previous request. Default is 1. |
Gene enrichment using Enrichr, also, you can now try adding a background.
Returns a list of data.frame of enrichment terms, p-values, ...
Wajid Jawaid wajid.jawaid@gmail.com
# data(input) # Load example input genes
# data(background) # Load example background genes
# dbs <- c("GO_Molecular_Function_2023", "GO_Cellular_Component_2023",
# "GO_Biological_Process_2023")
# if (getOption("enrichR.live")) {
# enriched1 <- enrichr(input, dbs)
# print(head(enriched1[[1]]))
# # Include background
# enriched2 <- enrichr(input, dbs, background = background)
# print(head(enriched2[[1]]))
# # Include background and add 'Overlap' info
# enriched3 <- enrichr(input, dbs, background = background, include_overlap = TRUE)
# print(head(enriched3[[1]]))
# }
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