set_corncob {benchdamic} | R Documentation |
Set the parameters for corncob differential abundance detection method.
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 )
pseudo_count |
add 1 to all counts if TRUE (default
|
formula |
an object of class |
phi.formula |
an object of class |
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
|
boot |
Boolean. Defaults to |
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
|
expand |
logical, if TRUE create all combinations of input parameters
(default |
A named list containing the set of parameters for DA_corncob
method.
# 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))