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.
pleio.q.fit(y, geno)matrix of multiple quantitative traits to test for pleiotropy on genotype vector. Rows are for subjects and columns are for traits.
vector of genotypes coded as dosage of a minor allele, 0,1,2. Allows imputed genotype dosage.
A list containing
the de-correlated genotype design matrix
inverse of x'x
estimated unconstrained beta coefficients for y traits based on ordinary least squares
number of traits (columns) in y
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)
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.