omnibusTest {midasHLA} | R Documentation

## Omnibus test

### Description

`OmnibusTest` calculates overall p-value for linear combination of variables using likelihood ratio test.

### Usage

    omnibusTest(
      object,
      omnibus_groups,
      placeholder = "term",
      correction = "bonferroni",
      n_correction = NULL
    )

### Arguments

`object` | An existing fit from a model function such as lm, glm and many others.
`omnibus_groups` | List of character vectors giving sets of variables for which omnibus test should be applied.
`placeholder` | String specifying term in `object`'s formula which should be substituted with variables during analysis.
`correction` | String specifying multiple testing correction method. See details for further information.
`n_correction` | Integer specifying number of comparisons to consider during multiple testing correction calculations. For Bonferroni correction it is possible to specify a number lower than the number of comparisons being made. This is useful in cases when knowledge about the biology or redundance of alleles reduces the need for correction. For other methods it must be at least equal to the number of comparisons being made; only set this (to non-default) when you know what you are doing!

### Details

Likelihood ratio test is conducted by comparing a model given in an `object` with an extended model, that is created by including the effect of variables given in `variables` as their linear combination.

### Value

Data frame with columns:

- "group" Omnibus group name

- "term" Elements of omnibus group added to base model

- "df" Difference in degrees of freedom between base and extended model

- "logLik" Difference in log likelihoods between base and extended model

- "statistic" Chisq statistic

- "p.value" P-value

- "p.adjusted" Adjusted p-value

### Examples

    midas <- prepareMiDAS(hla_calls = MiDAS_tut_HLA,
                          colData = MiDAS_tut_pheno,
                          experiment = "hla_aa")

    # define base model
    object <- lm(disease ~ term, data = midas)
    omnibusTest(object,
                omnibus_groups = list(
                  A_29 = c("A_29_D", "A_29_A"),
                  A_43 = c("A_43_Q", "A_43_R")
                ))

[Package midasHLA version 1.2.0 Index]