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Calculate enrichment of DE genes in a gene set Compute one‐sided hypergeometric p-values, z-scores, and combined scores for a list of differentially expressed genes (deg) against each entry in a list of gene sets (genesets). Internal function

Source: R/compute_hyper_enrich_bg.R
compute_hyper_enrich_bg.Rd

Calculate enrichment of DE genes in a gene set Compute one‐sided hypergeometric p-values, z-scores, and combined scores for a list of differentially expressed genes (deg) against each entry in a list of gene sets (genesets). 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

integer or character ("human", "mouse", or "geneset"). If "human", uses an approximate universe of 20 000 genes; if "mouse", 22 000; if "geneset", the total unique genes in genesets. You may also supply a custom integer (n) equal to the exact size of your tested universe.

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