geneSetEnrich {celda} | R Documentation |
Identify and return significantly-enriched terms for each gene module in a Celda object. Performs gene set enrichment analysis for Celda identified modules using the enrichR package.
geneSetEnrich(counts, celdaModel, databases, fdr = 0.05)
counts |
Integer count matrix. Rows represent genes and columns represent cells. Row names of the matrix should be gene names. |
celdaModel |
Celda object of class 'celda_G' or 'celda_CG'. |
databases |
Character vector. Name of reference database. Available
databases can be viewed by running |
fdr |
False discovery rate (FDR). Numeric. Cutoff value for adjusted p-value, terms with FDR below this value are considered significantly enriched. |
List of length 'L' where each member contains the significantly enriched terms for the corresponding module.
Ahmed Youssef
library(M3DExampleData) counts <- M3DExampleData::Mmus_example_list$data #subset 100 genes for fast clustering counts <- counts[1500:2000, ] #cluster genes into 10 modules for quick demo cm <- celda_G(counts = as.matrix(counts), L = 10, verbose = FALSE) gse <- geneSetEnrich(counts, cm, databases = c('GO_Biological_Process_2018','GO_Molecular_Function_2018'))