MAGENTAtest: MAGENTA test implementation

In ZAEDPolSl/intGSASNP: Integration Gene Set Analysis for SNP

Description

Performs a MAGENTA test on SNP p-values

Usage

MAGENTAtest(
  data,
  pathways = NA,
  int.method = "min",
  adjust.int = FALSE,
  int.cor.LD = FALSE,
  cutoff = 0.05,
  adjust.method = "BH",
  permutations = 1000
)

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
cutoff	enrichment p-value cutoff
adjust.method	multiple testing correction method
permutations	number of gene set permutations

Value

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

Examples

MAGENTAtest(data = example_dataset, pathways = pathway_library, int.method = "min", 
adjust.int = FALSE, int.cor.LD = FALSE, cutoff = 0.05, adjust.method = "BH", permutations = 1000)

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