aldex.senAnalysis: Sensitivity analysis using scale simulation

In ggloor/ALDEx_bioc: Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Sensitivity analysis using scale simulation

Description

Performs scale simulation over a range of values for gamma. Dirichlet samples are reused for computational convenience.

Usage

aldex.senAnalysis(
  aldex_clr,
  gamma,
  test = "t",
  effect = TRUE,
  include.sample.summary = FALSE,
  verbose = FALSE,
  iterate = FALSE,
  ...
)

Arguments

aldex_clr	An 'aldex.clr' object
gamma	A vector of positive numeric components. Used as the standard deviation of the scale simulation model.
test	A character string. Indicates which tests to perform. "t" runs Welch's t and Wilcoxon tests. "kw" runs Kruskal-Wallace and glm tests. "glm" runs a generalized linear model using a model.matrix. "corr" runs a correlation test using cor.test.
effect	A boolean. Toggles whether to calculate abundances and effect sizes.
include.sample.summary	A boolean. Toggles whether to include median clr values for each sample. Applies to effect = TRUE.
verbose	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large datasets. Applies to effect = TRUE.
iterate	A boolean. Toggles whether to iteratively perform a test. For example, this will use the results from an initial "t" routine to seed the reference (i.e., denominator of Geometric Mean calculation) for a second "t" routine.
...	Arguments to embedded method (e.g., glm or cor.test).

Value

A list of results. Each element corresponds to a single result for a given value of gamma

ggloor/ALDEx_bioc documentation built on Oct. 31, 2023, 1:13 a.m.