SampleSelector: SampleSelector

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

Description

The Sample Selector returns features of only those samples that have a drug response for the drug specified by the user's input for DrugName and are available for all chosen input data types. If a specific tissue is selected, the samples are reduced to cell lines of that tissue only.

Usage

SampleSelector(TrainObject, TrainingTissue, InputDataTypes)

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
TrainingTissue	Tissue type that the cell lines of the TrainObject should be of, such as "lung". Default should be "all" for pancancer analysis.
InputDataTypes	Data types of the TrainObject that are to be used to train the model, such as "GeneExpression", "Mutation", "CopyNumberVariation", "Methylation", "CancerType", etc.

Value

TrainObject

The TrainObject with only those samples that have the specified drug response and are available for all chosen input data types.

Examples

SampleSelector(GDSC, "pancreas", "GeneExpression")
SampleSelector(GDSC, "all", c("GeneExpression","Mutation"))

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