pleio.q.fit: Compute Intermediate Statisics for Testing Pleiotropy

In sinnweja/rpleio: Pleiotropy Test for Multiple Traits on a Genetic Marker

Compute Intermediate Statisics for Testing Pleiotropy

Description

Pre-compute statisics for testing pleiotropy, to be used in pleio.q.test and pleio.q.sequential. This is an earlier function for gaussian traits without covariates. The function pleio.glm.fit is more general, allowing for gaussian traits, and possibly adjusting covariates.

Usage

pleio.q.fit(y, geno)

Arguments

y	matrix of multiple quantitative traits to test for pleiotropy on genotype vector. Rows are for subjects and columns are for traits.
geno	vector of genotypes coded as dosage of a minor allele, 0,1,2. Allows imputed genotype dosage.

Details

The matrix y of traits is expected to have rows for subjects and columns for traits. The number of rows of y should match the length of vector geno. This function computes intermediate statistics that are subsequently used to test various hypotheses about pleiotropy. For technical details, Schaid et al. (Genetics, 2016)

Value

A list containing

x	the de-correlated genotype design matrix
xx.inv	inverse of x'x
beta.ols	estimated unconstrained beta coefficients for y traits based on ordinary least squares
n.traits	number of traits (columns) in y

Author(s)

Dan Schaid, Jason Sinnwell.

References

Schaid DJ, Tong X, Larrabee B, Kennedy RB, Poland GA, Sinnwell JP. Statistical Methods for Testing Genetic Pleiotropy. Genetics. 2016 Oct;204(2):483-497.

sinnweja/rpleio documentation built on Dec. 10, 2023, 10:13 p.m.