pleio.glm.fit: Compute Intermediate Statisics for Testing Pleiotropy
In pleio: Pleiotropy Test for Multiple Traits on a Genetic Marker

Description Usage Arguments Details Value Author(s) References

View source: R/pleio.glm.fit.R

Pre-compute statisics for testing pleiotropy, to be used in pleio.glm.test and pleio.glm.sequential

1	pleio.glm.fit(y, g, glm.family, x.all=NULL, x.index.list=NULL)

`y`	matrix of multiple traits to test for pleiotropy on genotype vector. Rows are for subjects and columns are for traits.
`g`	vector of genotypes coded as dosage of a minor allele, 0,1, and 2. Allows imputed genotype dosage.
`glm.family`	vector of strings corresponding to the type of phenotype for the columns of y. Types accepted are gaussian, binomial, and ordinal.
`x.all`	matrix of all covariates traits to adjust for the traits.
`x.index.list`	a list of vectors containing the index of the columns of x.all for which to be adjusted for each trait. The list must have the same number of vectors as there are traits in y. If one trait has no covarites, specify a vector containing 0 for that trait.

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 g. If adjusting traits by covarites in x.all, the x.index.list must be a list containing a vector of indices of the columns of x.all for each trait. If one trait does not have covariates and others do, then the vector for the trait with no covariate must be a vector containing the number 0. This function computes intermediate statistics that are subsequently used to test various hypotheses about pleiotropy. For technical details, Schaid et al. (2016, 2017)

A list containing

`theta`
`n.intercepts`
`n.coef.covar`
`n.parm`
`an.mat`
`n.traits`	number of traits (columns) in y

Dan Schaid, Jason Sinnwell.

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.

Schaid DJ, Tong X, Batzler A, Sinnwell JP, Qing J, Biernacka JM. Multivariate Generalized Linear Model for Genetic Pleiotropy. Under review.

pleio documentation built on May 2, 2019, 7:27 a.m.