timma (version 1.2.0)

sffsBinary: Model selection with sffs for the binary drug-target interaction data

Description

A function to select the most predictive targets with sffs for the binary drug-target interaction data using orignal maximization and minimization rules

Usage

sffsBinary(profile_data, sens, sp = 1, max_k = 2, loo = TRUE,
  verbosity = FALSE)

Arguments

profile_data

drug-target interaction data which is a matrix with drugs as row indexes and targets as column indexes.

sens

a drug sensitivity vector.

sp

an integer to specify the starting point for sequential forward floating search (sffs) search algorithm to navigate the target set space. By default, sp = 1.

max_k

an integer to sepcify the maximum number of targets that can be selected by the sffs algorithm. By default, max_k = 2. In practice it should not be over than 10 as the number of target combinations will increase exponentially.

loo

a logical value indicating whether to use the leave-one-out cross-validation in the model selection process. By default, loo = True.

verbosity

a boolean value to decide if the information should be displayed. If it is TRUE, the information will be displayed while the model is running. Otherwise, the information will not be displayed. By default, it is FALSE.

Value

• A list containing the following components:
• timma
  a list contains: the predicted efficacy matrix, prediction error and predicted drug sensitivity
• k_sel
  the indexes for selected targets

References

Tang J, Karhinen L, Xu T, Szwajda A, Yadav B, Wennerberg K, Aittokallio T. Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PLOS Computational Biology 2013; 9: e1003226.

Examples

data(tyner_interaction_binary)
data(tyner_sensitivity)
results<-sffsBinary(tyner_interaction_binary, tyner_sensitivity[, 1], max_k = 2)