GPATreeStage1: Implement the Stage 1 of the GPA-Tree Method

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

Description

This function will implement the stage 1 of the GPA-Tree method.

Usage

GPATreeStage1(gwasPval, annMat, initAlpha = 0.1)

Arguments

gwasPval	A matrix of M X 1 dimension where M is the number of SNPs. The matrix contains GWAS association p-values. Values must be between 0 and 1.
annMat	A matrix of binary annotations, where row and column correspond to SNPs and annotations, respectively.
initAlpha	Initial value for alpha estimate. Default is 0.1.

Value

This function returns a List including:

• num_iter_stage1: number of iterations taken for Stage 1 of GPA-Tree to converge.

• pi_stage1: predicted posterior probability of being a non-null SNP in Stage 1 of GPA-Tree Method.

• alpha_stage1: estimated alpha of GPA-Tree Method.

• beta_stage1: beta parameters from the linear model fitted at convergence of Stage 1 of GPA-Tree Method.

Author(s)

Aastha Khatiwada

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