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"))

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