getEnrichedPathways: Get enriched pathways based on marker genes from EnrichR.

In whtns/seuratTools: Tools for Managing Seurat Objects

Get enriched pathways based on marker genes from EnrichR.

Description

This function uses the enrichR API to look for enriched pathways in marker gene sets of samples and clusters.

Usage

getEnrichedPathways(
  object,
  column_cluster = "group",
  databases = c("GO_Biological_Process_2018", "GO_Cellular_Component_2018",
    "GO_Molecular_Function_2018", "KEGG_2016", "WikiPathways_2016", "Reactome_2016",
    "Panther_2016", "Human_Gene_Atlas", "Mouse_Gene_Atlas"),
  adj_p_cutoff = 0.05,
  max_terms = 100,
  URL_API = "http://amp.pharm.mssm.edu/Enrichr/enrich"
)

Arguments

object	Seurat object. about sample; defaults to 'sample'.
column_cluster	Column in [e-mail] that contains information about cluster; defaults to 'cluster'.
databases	Which databases to query. Use enrichR::listEnrichrDbs() to check what databases are available.
adj_p_cutoff	Cut-off for adjusted p-value of enriched pathways; defaults to 0.05,
max_terms	Save only first n entries of each database; defaults to 100.
URL_API	URL to send requests to (Enrichr API). Allows to overwrite default URL with an alternative taken from the Enrichr website in case the original is out-of-service; defaults to 'http://amp.pharm.mssm.edu/Enrichr/enrich'.

Details

Get enriched pathways based on marker genes from EnrichR.

Value

Seurat object with Enrichr results for samples and clusters stored in object@misc$enriched_pathways$enrichr

Author(s)

Roman Hillje, modified by Kevin Stachelek

Examples

pbmc <- readRDS(system.file("extdata/v1.2/seurat_pbmc.rds",
    package = "cerebroApp"
))
pbmc <- getEnrichedPathways(
    object = pbmc,
    column_sample = "sample",
    column_cluster = "seurat_clusters",
    databases = c("GO_Biological_Process_2018", "GO_Cellular_Component_2018"),
    adj_p_cutoff = 0.01,
    max_terms = 100,
    URL_API = "http://amp.pharm.mssm.edu/Enrichr/enrich"
)

whtns/seuratTools documentation built on Oct. 28, 2024, 7:18 a.m.