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

View source: R/stats.R

modelGeneExpression_significance_testing_wraperR Documentation

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.