ANOVA: Analysis of Variance

In computational-metabolomics/structToolbox: Data processing & analysis tools for Metabolomics and other omics

Analysis of Variance

Description

Analysis of Variance (ANOVA) is a univariate method used to analyse the difference among group means. Multiple test corrected p-values are computed to indicate significance for each feature.

Usage

ANOVA(alpha = 0.05, mtc = "fdr", formula, ss_type = "III", ...)

Arguments

alpha	(numeric) The p-value cutoff for determining significance. The default is 0.05.
mtc	(character) Multiple test correction method. Allowed values are limited to the following: "bonferroni": Bonferroni correction in which the p-values are multiplied by the number of comparisons. "fdr": Benjamini and Hochberg False Discovery Rate correction. "none": No correction. The default is "fdr".
formula	(formula) A symbolic description of the model to be fitted.
ss_type	(character) ANOVA sum of squares. Allowed values are limited to the following: "I": Type I sum of squares. "II": Type II sum of squares. "III": Type III sum of squares. The default is "III".
...	Additional slots and values passed to struct_class.

Details

This object makes use of functionality from the following packages:

• car

Value

A ANOVA object with the following output slots:

f_statistic	(data.frame) The value of the calculated statistic.
p_value	(data.frame) The probability of observing the calculated statistic if the null hypothesis is true.
significant	(data.frame) True/False indicating whether the p-value computed for each variable is less than the threshold.

Inheritance

A ANOVA object inherits the following struct classes:

⁠[ANOVA]⁠ >> ⁠[model]⁠ >> ⁠[struct_class]⁠

References

Fox J, Weisberg S (2019). An R Companion to Applied Regression, Third edition. Sage, Thousand Oaks CA. https://socialsciences.mcmaster.ca/jfox/Books/Companion/.

Examples

M = ANOVA(
      alpha = 0.05,
      mtc = "fdr",
      formula = y ~ x,
      ss_type = "III")

D = iris_DatasetExperiment()
M = ANOVA(formula=y~Species)
M = model_apply(M,D)

computational-metabolomics/structToolbox documentation built on Feb. 12, 2024, 2:15 a.m.