BAT | R Documentation |

Conducts tests of association between the loci in `G`

and the
untransformed phenotype `y`

, adjusting for the model matrix `X`

.

```
BAT(y, G, X = NULL, test = "Score", simple = FALSE)
```

`y` |
Numeric phenotype vector. |

`G` |
Genotype matrix with observations as rows, SNPs as columns. |

`X` |
Model matrix of covariates and structure adjustments. Should include an intercept. Omit to perform marginal tests of association. |

`test` |
Either Score or Wald. |

`simple` |
Return the p-values only? |

If `simple = TRUE`

, returns a vector of p-values, one for each column
of `G`

. If `simple = FALSE`

, returns a numeric matrix, including the
Wald or Score statistic, its standard error, the Z-score, and the p-value.

Direct INT

`DINT`

Indirect INT

`IINT`

Omnibus INT

`OINT`

```
set.seed(100)
# Design matrix
X <- cbind(1, stats::rnorm(1e3))
# Genotypes
G <- replicate(1e3, stats::rbinom(n = 1e3, size = 2, prob = 0.25))
storage.mode(G) <- "numeric"
# Phenotype
y <- as.numeric(X %*% c(1, 1)) + stats::rnorm(1e3)
# Association test
p <- BAT(y = y, G = G, X = X)
```

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