modelGeneExpression_significance_testing_wraper: Statistical testing of ridge regression estimates wrapper for...

In bkaczkowski/xcore: xcore expression regulators inference

Statistical testing of ridge regression estimates wrapper for modelGeneExpression

Description

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.

bkaczkowski/xcore documentation built on Jan. 26, 2024, 6:24 p.m.