create.classifier.univariate {SIMMS}

Trains and tests a univariate (per subnetwork module) survival model

Description

Trains a model on training datasets. Predicts the risk score for all the training & datasets, independently. This function also predicts the risk score for combined training datasets cohort and validation datasets cohort. The risk score estimation is done by multivariate models fit by fit.survivalmodel. The function also predicts risk scores for each of the top.n.features independently.

Usage

create.classifier.univariate(
  data.directory = ".",
  output.directory = ".",
  feature.selection.datasets = NULL,
  feature.selection.p.threshold = 0.05,
  training.datasets = NULL,
  validation.datasets = NULL,
  top.n.features = 25,
  models = c("1", "2", "3")
)

Arguments

data.directory

Path to the directory containing datasets as specified by feature.selection.datasets, training.datasets, validation.datasets

output.directory

Path to the output folder where intermediate and results files will be saved

feature.selection.datasets

A vector containing names of datasets used for feature selection in function derive.network.features()

feature.selection.p.threshold

One of the P values that were used for feature selection in function derive.network.features(). This function does not support vector of P values as used in derive.network.features() for performance reasons

training.datasets

A vector containing names of training datasets

validation.datasets

A vector containing names of validation datasets

top.n.features

A numeric value specifying how many top ranked features will be used for univariate survival modelling

models

A character vector specifying which of the models ('1' = N+E, '2' = N, '3' = E) to run

Value

The output files are stored under output.directory/output/

Author(s)

Syed Haider

Examples

# see package's main documentation