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MaAsLin3 analysis

Source: R/maaslin3.R
step_maaslin.Rd

MaAsLin 3 finds associations between microbiome meta-omics features and complex metadata. It uses a unified framework to test for both abundance (using linear models) and prevalence (using logistic regression).

Usage

step_maaslin(
  rec,
  min_abundance = 0,
  min_prevalence = 0.1,
  min_variance = 0,
  normalization = "TSS",
  transform = "LOG",
  max_significance = 0.1,
  random_effects = NULL,
  correction = "BH",
  standardize = TRUE,
  reference = NULL,
  median_comparison_abundance = TRUE,
  rarefy = FALSE,
  id = rand_id("maaslin"),
  engine_args = list()
)

Arguments

rec

A Recipe object. The step will be added to the sequence of operations for this Recipe. Execution requires add_model() before prep(); the step can be configured before adding the model.

min_abundance

The minimum abundance for each feature.

min_prevalence

The minimum percent of samples for which a feature is detected at minimum abundance.

min_variance

Keep features with variance greater than.

normalization

The normalization method to apply. Default: "TSS". Choices: "TSS", "CLR", "NONE".

transform

The transform to apply. Default: "LOG" (Base 2). Choices: "LOG", "PLOG", "NONE".

max_significance

The q-value threshold for significance.

random_effects

The random effects for the model (vector of character strings).

correction

The correction method for computing the q-value.

standardize

Apply z-score so continuous metadata are on the same scale.

reference

The factor to use as a reference for a variable with more than two levels provided as a string of 'variable,reference' semi-colon delimited.

median_comparison_abundance

Test abundance coefficients against a null value corresponding to the median coefficient for a metadata variable across the features. Recommended for relative abundance (default: TRUE).

rarefy

Boolean indicating if OTU counts must be rarefyed.

id

Unique, non-empty identifier for this step. DA step IDs must not use the reserved internal names taxa_id, contrast_id, comparison, contrast_type, var, effect, sum, .tax_order, .contrast_order or .effect_order. Other identifiers, including names such as .custom, are retained unchanged.

engine_args

Named lists of advanced arguments for the native fit or contrast stage. Arguments managed by dar or exposed above cannot be overridden.

Value

An object of class Recipe

See also

Other Diff taxa steps: step_aldex2(), step_aldex3(), step_ancom(), step_corncob(), step_deseq(), step_lefse(), step_linda(), step_rademu(), step_wilcox()

Examples

data(metaHIV_phy)

rec <- recipe(metaHIV_phy) |>
  add_model(~ RiskGroup2, targets = "RiskGroup2", tax_level = "Phylum")

rec_default <- step_maaslin(rec)

# Increase the minimum feature prevalence.
rec_filtered <- step_maaslin(rec, min_prevalence = 0.2)