calculate: Calculate overlap statistics

In AhmedMehdiLab/E.PAGE: Environmental Pathways Affecting Gene Expression

Calculate overlap statistics

Description

Calculate overlap statistics

Usage

calculate(input, annos, gs_annos, gs_genes, univ_size = NULL, org_db = NULL)

Arguments

input	output of process_input_text or process_input_seurat
annos	value from process_annotations
gs_annos	value from process_annotations
gs_genes	value from process_database
univ_size	optional: number of genes in universe; default calculated from gs_genes
org_db	optional: GO organism database e.g. org.Hs.eg.db::org.Hs.eg.db

Value

stats tibble: overlap statistics

matches list: names: annotations vector: matched genes

go NULL or output of clusterProfiler::enrichGO

Examples

## Not run: 
anno <- E.PATH::annotations
data <- E.PATH::database

input <- process_input_text("FCN1 0.1 FTL 0.8 CLU 0.05")
calc <- calculate(input, anno$annos, anno$gs_annos, data$gs_genes)

## End(Not run)

AhmedMehdiLab/E.PAGE documentation built on Aug. 21, 2022, 4:37 p.m.