set_MAST {benchdamic} | R Documentation

## set_MAST

### Description

Set the parameters for MAST differential abundance detection method.

### Usage

    set_MAST(
      pseudo_count = FALSE,
      rescale = c("median", "default"),
      design = NULL,
      coefficient = NULL,
      norm = "TSS",
      expand = TRUE
    )

### Arguments

`pseudo_count` | add 1 to all counts if TRUE (default `pseudo_count = FALSE`).
`rescale` | Rescale count data, per million if 'default', or per median library size if 'median' ('median' is suggested for metagenomics data).
`design` | The model for the count distribution. Can be the variable name, or a character similar to "~ 1 + group", or a formula, or a 'model.matrix' object.
`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_MAST` method.

### See Also

`DA_MAST`

### Examples

    # Set some basic combinations of parameters for MAST
    base_MAST <- set_MAST(design = ~ group, coefficient = "groupB")
    # Set a specific set of normalization for MAST (even of other packages!)
    setNorm_MAST <- set_MAST(design = ~ group, coefficient = "groupB",
        norm = c("TSS", "poscounts", "TMM"))
    # Set many possible combinations of parameters for MAST
    all_MAST <- set_MAST(pseudo_count = c(TRUE, FALSE), rescale = c("median",
        "default"), design = ~ group, coefficient = "groupB", norm = c("TSS",
        "poscounts"))

[Package benchdamic version 1.0.0 Index]