fold_change_int {structToolbox} | R Documentation |
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.
fold_change_int( alpha = 0.05, factor_name, threshold = 2, control_group = character(0), method = "geometric", ... )
alpha |
(numeric) The p-value cutoff for determining significance. The default is |
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 |
control_group |
(character) The level names of the groups used in the denominator (where possible) when computing fold change. One level for each factor, assumed to be in the same order as factor_name. The default is |
method |
(character) Fold change method. Allowed values are limited to the following:
The default is |
... |
Additional slots and values passed to |
A fold_change_int
object.
Lloyd GR, Weber RJM (2021). struct: Statistics in R Using Class-based Templates. R package version 1.3.1.
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)