FeatureSelector: Select the Genes that are used as Model Features

In JRC-COMBINE/FORESEE: A Tool for the Systematic Comparison of Translational Drug Response Modeling Pipelines

Description

The FeatureSelector selects a subset of features from all genes to be used for drug efficacy prediction.

Usage

FeatureSelector(TrainObject, TestObject, GeneFilter, DrugName)

Arguments

TrainObject	Object that contains all data needed to train a model, including molecular data (such as gene expression, mutation, copy number variation, methylation, cancer type, etc.) and drug response data
TestObject	Object that contains all data that the model is to be tested on, including molecular data (such as gene expression, mutation, copy number variation, methylation, cancer type, etc.) and drug response data
GeneFilter	Set of genes to be considered for training the model, such as all, a certain percantage based on variance or p-value, specific gene sets like landmark genes, gene ontologies or pathways, etc. The option 'variance' removes the 20 The option 'pvalue' removes the 20 The option 'landmarkgenes' uses the L1000 gene set downloaded from CLUE Command App The option 'ontology' uses a specific set of genes included in the ontology associated with the drug The option 'pathway' uses a specific set of genes included in the pathway associated with the drug The option 'all' keeps all genes as features The function 'listInputOptions("FeatureSelector")' returns a list of the possible options. Instead of choosing one of the implemented options, a user-defined function can be used as an input. If the user inserts a list as an input, the list is considered as chosen features.
DrugName	Name of the drug whose efficacy is supposed to be predicted with the model. It is used in 'ontology' or 'pathway' GeneFilters.

Value

TrainObject	The TrainObject with the selected gene set as features.
TestObject	The TestObject with homogenized features according to the chosen TrainObject.

Examples

FeatureSelector(GDSC,GSE6434,"variance","Docetaxel")
FeatureSelector(GDSC,GSE6434,"pathway","Tamoxifen")

JRC-COMBINE/FORESEE documentation built on Jan. 24, 2020, 1:19 a.m.