cnvGSA (version 1.10.0)

cnvGSAFisher: CNV/gene-set association using Fisher Exact Test

Description

Performs the CNV/gene-set association using the Fisher Exact Test.

Usage

cnvGSAFisher( input )

Arguments

input

Object of class CnvGSAInput.

Value

Outputs an object of class CnvGSAOutput containing detailed enrichment results as well as gene-centric and global burden statistics.

Details

Whenever a subject has at least one gene in a gene-set affected by a rare variant, a perturbation score of 1 is assigned to the (subject, gene-set) pair; for each gene-set, subject counts are tested vs. control counts using the Fisher Exact Test (FET). Significant gene-sets will have a significantly high count in cases compared to controls. Statistical reports on burden are also generated.

Examples

library("cnvGSAdata")
data("cnvGSA_input_example")
output <- cnvGSAFisher(input)