set_corncob {benchdamic} | R Documentation

## set_corncob

### Description

Set the parameters for corncob differential abundance detection method.

### Usage

    set_corncob(
      pseudo_count = FALSE,
      formula = NULL,
      phi.formula = NULL,
      formula_null = NULL,
      phi.formula_null = NULL,
      test = c("Wald", "LRT"),
      boot = FALSE,
      coefficient = NULL,
      norm = "TSS",
      expand = TRUE
    )

### Arguments

`pseudo_count` | add 1 to all counts if TRUE (default `pseudo_count = FALSE`).
`formula` | an object of class `formula` without the response: a symbolic description of the model to be fitted to the abundance.
`phi.formula` | an object of class `formula` without the response: a symbolic description of the model to be fitted to the dispersion.
`formula_null` | Formula for mean under null, without response
`phi.formula_null` | Formula for overdispersion under null, without response
`test` | Character. Hypothesis testing procedure to use. One of `"Wald"` or `"LRT"` (likelihood ratio test).
`boot` | Boolean. Defaults to `FALSE`. Indicator of whether or not to use parametric bootstrap algorithm. (See `pbWald` and `pbLRT`).
`coefficient` | The coefficient of interest as a single word formed by the variable name and the non reference level. (e.g.: 'ConditionDisease' if the reference level for the variable 'Condition' is 'control').
`norm` | name of the normalization method used to compute the normalization factors to use in the differential abundance analysis. If `norm` is equal to "TMM", "TMMwsp", "RLE", "upperquartile", "posupperquartile", "CSSmedian", "CSSdefault", "TSS" the scaling factors are automatically transformed into normalization factors.
`expand` | logical, if TRUE create all combinations of input parameters (default `expand = TRUE`)

### Value

A named list containing the set of parameters for `DA_corncob` method.

### See Also

`DA_corncob`

### Examples

    # Set some basic combinations of parameters for corncob
    base_corncob <- set_corncob(formula = ~ group, phi.formula = ~ group,
        formula_null = ~ 1, phi.formula_null = ~ group, coefficient = "groupB")
    # Set a specific set of normalization for corncob (even of other packages!)
    setNorm_corncob <- set_corncob(formula = ~ group, phi.formula = ~ group,
        formula_null = ~ 1, phi.formula_null = ~ group, coefficient = "groupB",
        norm = c("TMM", "TSS", "poscounts"))
    # Set many possible combinations of parameters for corncob
    all_corncob <- set_corncob(pseudo_count = c(TRUE, FALSE), formula = ~ group,
        phi.formula = ~ group, formula_null = ~ 1, phi.formula_null = ~ group,
        coefficient = "groupB", boot = c(TRUE, FALSE))

[Package benchdamic version 1.0.0 Index]