GSEASNPtest: GSEASNP test implementation

In ZAEDPolSl/intGSASNP: Integration Gene Set Analysis for SNP

Description

Performs an GSEASNP test on SNP p-values

Usage

GSEASNPtest(
  data,
  pathways = NA,
  adjust.method = "BH",
  permutations = 10000,
  cores = 2
)

Arguments

data	input dataframe with column names: "snp", "entrez", "p.value"
pathways	object containing a list of GENES and a list of MODULES
adjust.method	multiple testing correction method
permutations	number of gene set permutations
cores	number of cores; default is 2

Value

A data frame with module names, calculated p-value, and additional statistics.

Examples

GSEASNPtest(data = example_dataset, pathways = pathway_library, adjust.method = "BH", 
permutations = 10000)

ZAEDPolSl/intGSASNP documentation built on Dec. 18, 2021, 8:24 p.m.