Calculate confusion matrix for cross-validation. — calcConfusionCv • metapredict

Calculate a confusion matrix based on predictions from cross-validation.

Usage

calcConfusionCv(
  cvFit,
  lambda,
  ematMerged,
  sampleMetadata,
  className = "class",
  classLevels = NA
)

Arguments

cvFit: cv.glmnet object from metapredictCv().
lambda: value of lambda at which to use predictions.
ematMerged: matrix of gene expression for genes by samples.
sampleMetadata: data.frame of sample metadata.
className: name of column in sampleMetadata containing the true labels.
classLevels: Order of classes in the confusion matrix. If NA (default), then the function uses the order in cvFit.

Value

An object of class table.