runFAIMS: Run a standard analysis given a FAIMS object and class labels

In mattdneal/FAIMSToolkit: Tools to aid in the analysis of FAIMS data

Description

Run a standard analysis given a FAIMS object and class labels

Usage

runFAIMS(FAIMSObject, targetValues, models = c("rf", "glmnet",
  "svmRadial", "svmLinear", "gbm", "nnet", "glm"),
  modelSelectFolds = NULL, modelSelectScores = NULL,
  bestModelFolds = NULL, bestModelScores = NULL, waveletData = NULL,
  SGoF = TRUE, nKeep = TRUE, extraData = NULL)

Arguments

FAIMSObject	a FAIMS object
targetValues	class labels
models	a list of caret::train models
modelSelectFolds	pre-generated folds for model selection
modelSelectScores	pre-generated scores for model selection
bestModelFolds	pre-generated folds for best model assessment
bestModelScores	pre-generated scores for best model assessment
waveletData	pre-computed wavelet data
SGoF	Select variables using sequential goodness of fit? (only for PCA analysis)
nKeep	Select variables using keep top N?
extraData	Additional data to feed to the classifier

Value

A list of results (see out$bestModelSummary and out$modelSelectSummary for a summary of results)

mattdneal/FAIMSToolkit documentation built on May 21, 2019, 12:57 p.m.