fisher_test: Fisher's exact test

In linnykos/eSVD2: eSVD2 for performing the eSVD-DE for cohort-wide differential expression analysis

Fisher's exact test

Description

Perform a Fisher's exact test. This formula is from https://www.pathwaycommons.org/guide/primers/statistics/fishers_exact_test/

Usage

fisher_test(set1_genes, set2_genes, all_genes, verbose = 0)

Arguments

set1_genes	A vector of characters of your resulting gene list
set2_genes	A vector of characters of a gene list you are comparing against
all_genes	A vector of characters of all the genes in your "universe". This should include all the genes in set1_genes and set2_genes.
verbose	Numeric

Value

A list of: pvalue for the p-value, set_bg_len for the number of genes in all_genes but not in set2_genes, set_overlap_len for the number of genes in both set1_genes and set2_genes, set1_len for number of genes in set1_genes, and set2_len for number of genes in set2_genes.

linnykos/eSVD2 documentation built on July 17, 2024, 12:01 a.m.