Get enriched pathways based on marker genes from EnrichR.

Source: R/getEnrichedPathways.R

This function uses the enrichR API to look for enriched pathways in marker gene sets of all available grouping variables.

getEnrichedPathways(
  object,
  marker_genes_input = "cerebro_seurat",
  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://maayanlab.cloud/Enrichr"
)

Arguments

object

Seurat object with marker genes calculated by getMarkerGenes.
marker_genes_input

Name of list of marker gene tables that will be used as input. This could be the "name" parameter used in getMarkerGenes(). Enriched pathways will be calculated for every group level of every grouping variable. Defaults to "cerebro_seurat".
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://maayanlab.cloud/Enrichr'.

Value

Seurat object with Enrichr results for all provided grouping variables, stored in object@misc$enriched_pathways$<marker_genes_input>_enrichr

Examples

pbmc <- readRDS(system.file("extdata/v1.3/pbmc_seurat.rds",
  package = "cerebroApp"))
pbmc <- getEnrichedPathways(
  object = pbmc,
  marker_genes_input = 'cerebro_seurat',
  databases = c('GO_Biological_Process_2018','GO_Cellular_Component_2018'),
  adj_p_cutoff = 0.01,
  max_terms = 100,
  URL_API = 'http://maayanlab.cloud/Enrichr'
)

#> [17:53:24] Found 2 groups: sample, seurat_clusters
#> [17:53:24] Get enriched pathways for group `sample`...
#> [17:53:27] 5 pathways passed the thresholds across all group levels and databases.
#> [17:53:27] Get enriched pathways for group `seurat_clusters`...
#> [17:53:29] 70 pathways passed the thresholds across all group levels and databases.