set_limma {benchdamic} | R Documentation |
Set the parameters for limma differential abundance detection method.
set_limma( pseudo_count = FALSE, design = NULL, coef = 2, norm = c("TMM", "TMMwsp", "RLE", "upperquartile", "posupperquartile", "none"), weights_logical = FALSE, expand = TRUE )
pseudo_count |
add 1 to all counts if TRUE (default
|
design |
character name of the metadata columns, formula, or design matrix with rows corresponding to samples and columns to coefficients to be estimated. |
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 |
weights_logical |
logical vector, if TRUE a matrix of observational
weights will be used for differential abundance analysis (default
|
expand |
logical, if TRUE create all combinations of input parameters
(default |
A named list containing the set of parameters for DA_limma
method.
# Set some basic combinations of parameters for limma base_limma <- set_limma(design = ~ group, coef = 2) # Set a specific set of normalization for limma (even of other packages!) setNorm_limma <- set_limma(design = ~ group, coef = 2, norm = c("TMM", "poscounts")) # Set many possible combinations of parameters for limma all_limma <- set_limma(pseudo_count = c(TRUE, FALSE), design = ~ group, coef = 2, weights_logical = c(TRUE,FALSE))