differential_pathway: Find differential pathways with enrichR

In vallotlab/IDclust: Iterative Differential Clustering for single-cell

Find differential pathways with enrichR

Description

Find differential pathways with enrichR

Usage

differential_pathway(
  genes,
  qval.th = 0.1,
  website = c("Enrichr", "FlyEnrichr", "WormEnrichr", "YeastEnrichr", "FishEnrichr")[1],
  databases = c("MSigDB_Hallmark_2020", "GO_Molecular_Function_2021",
    "MSigDB_Oncogenic_Signatures"),
  order_by_database = TRUE
)

Arguments

genes	A character vector containing at least 10 genes
qval.th	A numeric specifying the adjusted p.value below which a pathway is considered as significantly enriched
website	site requested
databases	(Required). Character vector of databases to search. See https://maayanlab.cloud/Enrichr/ for available databases.
order_by_database	A logical. If TRUE, row will appear in the order of the databases vector, then within each database are sorted by adjusted pvalue.

Value

A dataframe with enriched pathways.

References

Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013). https://doi.org/10.1186/1471-2105-14-128

Examples

pathways <- differential_pathway(
c("Runx1", "Gfi1", "Gfi1b", "Spi1", "Gata1", "Kdr"))

vallotlab/IDclust documentation built on July 5, 2024, 3:26 p.m.