Description Usage Arguments Details Examples
View source: R/getEnrichedPathways.R
This function uses the enrichR API to look for enriched pathways in marker gene sets of samples and clusters.
1 2 3 4 5 6 7 | 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")
|
object |
Seurat object. |
column_sample |
Column in object@meta.data that contains information about sample; defaults to 'sample'. |
column_cluster |
Column in object@meta.data 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'. |
Get enriched pathways based on marker genes from EnrichR.
1 2 3 4 5 6 7 8 9 | 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'
)
|
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