iGSEA4GWAStest: iGSEA4GWAS test implementation

In ZAEDPolSl/intGSASNP: Integration Gene Set Analysis for SNP

Description

Performs an iGSEA4GWAS test on SNP p-values

Usage

iGSEA4GWAStest(
  data,
  pathways = NA,
  int.method = "min",
  adjust.int = FALSE,
  int.cor.LD = FALSE,
  adjust.method = "BH",
  permutations = 1000,
  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
int.method	integration method (either "min", "fisher', or "stouffer")
adjust.int	flag for multiple testing correction in integration
int.cor.LD	flag for LD correction in integration
adjust.method	multiple testing correction method
permutations	number of gene set permutations
cores	number of cores; if cores > 2 use parallel computing

Value

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

Examples

iGSEA4GWAStest(data = example_dataset, pathways = pathway_library, int.method = "min", 
adjust.int = FALSE, int.cor.LD = FALSE, adjust.method = "BH", permutations = 10000)

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