set_metagenomeSeq {benchdamic} | R Documentation |
Set the parameters for metagenomeSeq differential abundance detection method.
set_metagenomeSeq( pseudo_count = FALSE, design = NULL, coef = 2, norm = c("CSSmedian", "CSSdefault"), expand = TRUE )
pseudo_count |
add 1 to all counts if TRUE (default
|
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 |
expand |
logical, if TRUE create all combinations of input parameters
(default |
A named list containing the set of parameters for
DA_metagenomeSeq
method.
# 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"))