Statistical testing of ridge regression estimates wrapper for modelGeneExpression — modelGeneExpression_significance_testing

Internal function used in modelGeneExpression. It runs ridgePvals parallelly across signatures and samples as specified by experiment design.

Usage

modelGeneExpression_significance_testing_wraper(
  mae,
  yname,
  uname,
  xnames,
  groups,
  standardize,
  regression_models
)

Arguments

mae: MultiAssayExperiment object such as produced by prepareCountsForRegression.
yname: string indicating experiment in mae to use as the expression input.
uname: string indicating experiment in mae to use as the basal expression level.
xnames: character indicating experiments in mae to use as molecular signatures.
groups: factor representation of design matrix.
standardize: logical flag indicating if the molecular signatures should be scaled. Advised to be set to TRUE.
regression_models: Named list with elements corresponding to signatures specified in xnames. Each of these is a list holding 'cv.glmnet' objects corresponding to each sample. Usually returned by modelGeneExpression_ridge_regression_wraper.

Value

Named list with elements corresponding to signatures specified in xnames. Each of these is a list holding data.frame of signature's p-values and test statistics estimated for each sample.