modelGeneExpression_ridge_regression_wraper: Ridge regression wrapper for modelGeneExpression

In bkaczkowski/xcore: xcore expression regulators inference

Ridge regression wrapper for modelGeneExpression

Description

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

Usage

modelGeneExpression_ridge_regression_wraper(
  mae,
  yname,
  uname,
  xnames,
  groups,
  standardize,
  parallel,
  precalcmodels,
  ...
)

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.
parallel	parallel argument to internally used cv.glmnet function. Advised to be set to FALSE as it might interfere with parallelization used in modelGeneExpression.
precalcmodels	optional list of precomputed 'cv.glmnet' objects for each molecular signature and sample. The elements of this list should be matching the xnames vector. Each of those elements should be a named list holding 'cv.glmnet' objects for each sample. If provided those models will be used instead of running regression from scratch.
...	arguments passed to glmnet::cv.glmnet.

Value

Named list with elements corresponding to signatures specified in xnames. Each of these is a list holding 'cv.glmnet' objects corresponding to each sample.

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