gcat {gcatest} | R Documentation

## 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)

[Package gcatest version 1.20.0 Index]