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

In romanhaa/cerebroPrepare: Export data for visualization in Cerebro.

Description

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

Usage

getEnrichedPathways(object, column_sample = "sample",
  column_cluster = "cluster",
  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.
column_sample	Column in [e-mail] that contains information 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.

Examples

seurat <- getEnrichedPathways(
  object = seurat,
  column_sample = 'sample',
  column_cluster = 'cluster',
  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'
)

romanhaa/cerebroPrepare documentation built on Oct. 17, 2019, 4:01 p.m.