getEnrichedPathways: Get enriched pathways based on marker genes from EnrichR.
In romanhaa/cerebroApp: Interactive visualization of scRNA-seq data with Cerebro

Description Usage Arguments Value Examples

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"
)

`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'.

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

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'
)