fold_change_int: Fold change for interactions between factors

In structToolbox: Data processing & analysis tools for Metabolomics and other omics

Description

For more than one factor the fold change calculation is extended to include all combinations of levels (interactions) of all factors. Paired fold changes are not possible for this computation.

Usage

fold_change_int(
  alpha = 0.05,
  factor_name,
  threshold = 2,
  control_group = character(0),
  ...
)

Arguments

alpha	(numeric) The p-value cutoff for determining significance. The default is 0.05.
factor_name	(character) The name of a sample-meta column to use.
threshold	(numeric) The fold change threshold for labelling features as significant. The default is 2.
control_group	(character) The level name of the group used in the denominator (where possible) when computing fold change. The default is character(0).
...	Additional slots and values passed to struct_class.

Value

A fold_change_int object.

References

Lloyd GR, Weber RJM (????). struct: Statistics in R Using Class-based Templates. R package version 1.1.2.

Examples

D = MTBLS79_DatasetExperiment()
D=D[,1:10,drop=FALSE]
M = filter_smeta(mode='exclude',levels='QC',factor_name='class') +
    fold_change_int(factor_name=c('class','batch'))
M = model_apply(M,D)

structToolbox documentation built on Nov. 8, 2020, 6:54 p.m.