set_metagenomeSeq {benchdamic} | R Documentation

## set_metagenomeSeq

### Description

Set the parameters for metagenomeSeq differential abundance detection method.

### Usage

    set_metagenomeSeq(
      pseudo_count = FALSE,
      design = NULL,
      coef = 2,
      norm = c("CSSmedian", "CSSdefault"),
      expand = TRUE
    )

### Arguments

`pseudo_count` | add 1 to all counts if TRUE (default `pseudo_count = FALSE`).
`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.
`coef` | integer or character index vector indicating which coefficients of the linear model are to be tested equal to zero.
`norm` | name of the normalization method used to compute the scaling factors to use in the differential abundance analysis. If `norm` is equal to "ratio", "poscounts", or "iterate" the normalization factors are automatically transformed into scaling 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_metagenomeSeq` method.

### See Also

`DA_metagenomeSeq`

### Examples

    # Set some basic combinations of parameters for metagenomeSeq
    base_mgs <- set_metagenomeSeq(design = ~ group, coef = 2)
    # Set a specific set of normalization for metagenomeSeq (even of other
    # packages!)
    setNorm_mgs <- set_metagenomeSeq(design = ~ group, coef = 2,
        norm = c("CSSmedian", "TMM"))
    # Set many possible combinations of parameters for metagenomeSeq
    all_mgs <- set_metagenomeSeq(pseudo_count = c(TRUE, FALSE), design = ~ group,
        coef = 2, norm = c("CSSmedian", "CSSdefault", "TMM", "TSS"))

[Package benchdamic version 1.0.0 Index]