GetTestMetaFeatures: Computes the metafeatures for each sample and model in the...

In ncats/MultiOmicsGraphPrediction: Network-Based Ensemble Prediction from IntLIM Predictors

Computes the metafeatures for each sample and model in the testing data.

Description

Computes the metafeatures for each sample and model in the testing data.

Usage

GetTestMetaFeatures(
  predictionsTrain,
  predictionsTest,
  inputDataTrain,
  inputDataTest,
  metaFeatureList = c("pdf", "localerr", "globalerr", "pathway", "reaction",
    "interactionpval", "interactioncoef", "analytecoef"),
  modelStats = "",
  k = k,
  eigStep = 10,
  alphaMin = 0,
  alphaMax = 1,
  alphaStep = 0.1,
  stype = "",
  colIdInd = "",
  colIdOut = ""
)

Arguments

predictionsTrain	Prediction data frame for training data, where rows are samples, and columns are predictors.
predictionsTest	Prediction data frame for testing data, where rows are samples, and columns are predictors.
inputDataTrain	The training data (in IntLimData format).
inputDataTest	The testing data (in IntLimData format).
metaFeatureList	A list of metafeatures to compute.
modelStats	A data frame that includes the interaction p-values and interaction coefficients for each pair (such as the one output by IntLIM's ProcessResults function)
k	The number of nearest neighbors to consider in localerr.
eigStep	The number of eigenvectors to step by during the evaluation in localerr. Note that this must be less than the number of samples in localerr. Default = 10.
alphaMin	The lowest value of alpha to investigate in localerr. Default = 0.
alphaMax	The highest value of alpha to investigate in localerr. Default = 1.
alphaStep	The value of alpha to step by during the evaluation in localerr. Default = 0.1.
stype	Phenotype or outcome to use in models.
colIdInd	The ID of the column that has the analyte ID's for the independent variable. If blank, then the existing ID's are used.
colIdOut	The ID of the column that has the analyte ID's for the outcome variable. If blank, then the existing ID's are used.

Value

A list of data frames (one for each sample) with predictor importance measured according to the listed criteria (one column per metric, one row per predictor).

ncats/MultiOmicsGraphPrediction documentation built on Aug. 23, 2023, 9:19 a.m.