Calculate enrichment of DE genes in a gene set Internal function

Calculate enrichment of DE genes in a gene set Internal function

Usage

compute_hyper_enrich_bg(deg = NULL, genesets = NULL, background = "human")

Arguments

deg

vector of differentially expressed genes

genesets

list of genes per pathway from enrichr

background

defaults to the number of genes in the geneset, otherwise a number of genes (integer) or species

Value

enrichment stats

Examples

data(mini_mac)
treatment_samples="Staurosporine_0.1"
control_samples<-"DMSO_0"
top_table <- compute_single_de(mini_mac, treatment_samples, control_samples,
method = "limma_voom")
top_genes <- top_table$gene[top_table$p_value_adj<0.01]
data(genesets)
results <- compute_hyper_enrich_bg(top_genes, genesets)
head(results)
#>                                        Term Overlap    P.value Adjusted.P.value
#> Androgen Response         Androgen Response   1/100 0.01985198        0.0394069
#> IL-2/STAT5 Signaling   IL-2/STAT5 Signaling   1/199 0.03921281        0.0394069
#> Apical Junction             Apical Junction   1/200 0.03940690        0.0394069
#> Xenobiotic Metabolism Xenobiotic Metabolism   1/200 0.03940690        0.0394069
#>                       Genes Combined.Score
#> Androgen Response     ACTN1       27.16313
#> IL-2/STAT5 Signaling   AHCY       15.58983
#> Apical Junction       ACTN1       15.52386
#> Xenobiotic Metabolism  AHCY       15.52386