View source: R/interpretation.R
top_enriched_pathways | R Documentation |
Find enriched pathways in marker genes of IDclust
top_enriched_pathways( IDC_DA, top = 1, qval.th = 0.1, gene_col = "gene", website = c("Enrichr", "FlyEnrichr", "WormEnrichr", "YeastEnrichr", "FishEnrichr")[1], databases = c("MSigDB_Hallmark_2020", "GO_Molecular_Function_2021", "MSigDB_Oncogenic_Signatures"), order_by_database = TRUE, max_genes_enriched = 1000 )
IDC_DA |
A data.frame of differential features at each
clustering iteration produced by |
top |
An integer specifying the number of top pathways to retrieve per cluster. |
qval.th |
A numeric specifying the adjusted p.value below which a pathway is considered as significantly enriched |
gene_col |
A character specifying the column in which to retrieve the gene / feature name. |
website |
site requested |
databases |
(Required). Character vector of databases to search. See https://maayanlab.cloud/Enrichr/ for available databases. |
order_by_database |
A logical. If TRUE, row will appear in the order of the databases vector, then within each database are sorted by adjusted pvalue. |
max_genes_enriched |
An integer specifying the maximum number of genes per cluster to enrich. If there are more than max_genes_enriched genes in the list, will keep only the top max_genes_enriched genes for enrichment. |
if(requireNamespace("enrichR")){ #scRNA data("IDC_DA_scRNA", package = "IDclust") library(enrichR) top_enriched_pathways( IDC_DA_scRNA, top = 1, gene_col = "gene", qval.th = 0.1) #scEpigenomics data("scExp", package = "IDclust") data("IDC_DA_scEpigenomics", package = "IDclust") # We must first add the gene information to the DA list: IDC_DA_scEpigenomics = add_gene_to_DA_list( scExp = scExp, IDC_DA = IDC_DA_scEpigenomics, feature_ID_col = "ID", gene_col = "Gene", distanceToTSS = 1000, split = TRUE, split_char = ", " ) top_enriched_pathways( IDC_DA_scEpigenomics, top = 1, gene_col = "Gene", qval.th = 0.1 ) }
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