hipoeigen: HIPO eigendecomposition

In gqi/hipo: Heritability Informed Power Optimization (HIPO)

Description

Performs HIPO eigendecomposition and calculates the z statistics and p-values of HIPO components.

Usage

hipoeigen(sumstats.all, traitvec, coherit.mat, ldscint.mat, HIPOD.num = 2,
  truncate = NULL)

Arguments

sumstats.all	Summary statitics of all individual traits, first output of preprocess().
traitvec	Vector of trait names, second output of preprocess().
coherit.mat	Genetic covariance matrix.
ldscint.mat	LD score regression intercept matrix.
HIPOD.num	Number of HIPO components to calculate z stats and p-value for.
truncate	Use only for high-dimensional phenotypes. If NULL, use the full coherit.mat and ldscint.mat; if a decimal, truncate the eigenvectors of ldscint.mat with eigenvalues < truncate*(max eigenvalue of ldscint.mat). Recommended 0.05.

Value

A list that contains

sumstats.all	A data.frame containing the summary statistics of all individual traits.
coherit.mat	Genetic covariance matrix.
ldscint.mat	Matrix of LD score regression intercepts.
eigenvalue	Eigenvalues from HIPO eigendecomposition. Proportional to the average non-centrality parameter.
HIPOD.mat	A matrix of which the columns are the HIPO components.

gqi/hipo documentation built on May 18, 2019, 8:12 p.m.