Get differential metabolites with log fold-changes and adjusted pvalues based on input comparison groups — DiffMetabolites • damR

Fits model on the full input dataset with limma

Usage

DiffMetabolites(
  cleanData,
  groups = NULL,
  contrastLevel = "Group",
  repeated_measures = "no"
)

Arguments

cleanData: The QC'd and imputed data.frame
groups: Vector of groups names to contrast. Defaults to the unique elements of the Group column but the column used can be specified using contrastLevel.
contrastLevel: The column from the data containing groups levels, usually "Group".
repeated_measures: Were there repeated measures?

Value

LogFC and adjusted P-values of limma::topTable() for each contrast