set_MAST: set_MAST

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

set_MAST

Description

Set the parameters for MAST differential abundance detection method.

Usage

set_MAST(
  assay_name = "counts",
  pseudo_count = FALSE,
  rescale = c("median", "default"),
  design = NULL,
  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).
rescale	Rescale count data, per million if 'default', or per median library size if 'median' ('median' is suggested for metagenomics data).
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.
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_MAST method.

See Also

DA_MAST

Examples

# Set some basic combinations of parameters for MAST
base_MAST <- set_MAST(design = ~ group, coefficient = "groupB")
# Set many possible combinations of parameters for MAST
all_MAST <- set_MAST(pseudo_count = c(TRUE, FALSE), rescale = c("median",
    "default"), design = ~ group, coefficient = "groupB")

mcalgaro93/benchdamic documentation built on Nov. 23, 2024, 5:06 p.m.