gcatest (version 1.2.2)

gcat: Genotype Conditional Association TEST

Description

Performs the GCAT test for association between SNPs and trait, and returns the p-values.

Usage

gcat(X, LF, trait, adjustment = NULL)
gcatest(X, LF, trait, adjustment = NULL)
gcat.stat(X, LF, trait, adjustment = NULL)

Arguments

X

a matrix of SNP genotypes, i.e. an integer matrix of 0's, 1's, and 2's. Sparse matrices of class Matrix are not supported (yet).

LF

matrix of logistic factors outputed from function lfa

trait

vector

adjustment

matrix of adjustment variables

Value

• vector of p-values

Functions

• gcatest:
• gcat.stat: returns the association statistics instead of the p-value.

References

Song, M, Hao, W, Storey, JD (2015). Testing for genetic associations in arbitrarily structured populations. Nat. Genet., 47, 5:550-4.

Examples

library(lfa)
LF = lfa(sim_geno, 3)
gcat_p = gcat(sim_geno, LF, sim_trait)
gcat_stat = gcat.stat(sim_geno, LF, sim_trait)