set_corncob: set_corncob

In mcalgaro93/benchdamic: Benchmark of differential abundance methods on microbiome data

set_corncob

Description

Set the parameters for corncob differential abundance detection method.

Usage

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

Arguments

assay_name	the name of the assay to extract from the TreeSummarizedExperiment object (default assayName = "counts"). Not used if the input object is a phyloseq.
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').
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 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))

mcalgaro93/benchdamic documentation built on Nov. 28, 2024, 2:16 p.m.