assoc: Association mapping

In asthakhatiwada/GPATree: A package to implement the GPA-Tree method

Description

This function will implement association mapping for the GPA-Tree model.

Usage

## S4 method for signature 'GPATree'
assoc(object, FDR = 0.05, fdrControl = "global")

Arguments

object	An object of class GPATree.
FDR	FDR level. Value has to be between 0 and 1.
fdrControl	Method to control FDR. Possible values are "global" (global FDR control) and "local" (local FDR control).

Value

Returns a MX2 matrix where the row represents SNPs, the fist column indicates the association between each SNP and phenotype, and the second column indicates the leaf in which the SNP falls

Author(s)

Aastha Khatiwada

Examples

## Not run: 
library(GPATree)

# load GPATree example data
data(GPATreeExampleData)

#fitting the GPATree model
fit <- GPATree(GPATreeExampleData$gwasPval, GPATreeExampleData$annMat)

# pruning the GPATree model fit
assoc.fit <- assoc(fit, FDR = 0.05, fdrControl = "global")

## End(Not run)

asthakhatiwada/GPATree documentation built on March 8, 2021, 5:29 a.m.