# Target Inhibition Interaction using Maximization and Minimization Averaging

## Documentation for package ‘timma’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

timma-package | Target Inhibition inference using Maximization and Minimization Averaging
binarizeDrugTargets | Binarize the drug target profile data
binarySet | Search for supersets and subsets
ci | The combination index extracted from Figure 1B of the Miller study
davis | Drug-target profile for 72 drugs and 442 targets.
dec2bin | Convert decimal values to binary values
drawGraph | Draw graph function
drugRank | Generate the list of ranked drug combinations
findSameCol | Find the same column from a matrix
findSameSet | Find the same columns from two matrices
floating2 | Filter targets
getBinary | Binary set for multiclass data
getBinary1 | Weighted binary set for multiclass data
graycode2 | Graycode Function
graycode3 | Gray code function for matrix indexes
graycodeNames | Names for the predicted sensitivity matrix
grays | Generate gray code
kiba | Kiba interaction data
maxcpp | Search for the max values of 3D matrix in cpp
maxcpp1 | Search for the max values of 2D matrix in cpp
miller_drugs | A drug list from Miller study
miller_drug_response | The single drug does-response data from the Miller study
miller_interaction_binary | The binarized drug-target data for the Miller drugs
miller_sensitivity | The scaled drug sensitivity data for the Miller drugs
miller_targets | The curated drug-target data for the Miller drugs
mincpp | Search for the min values of 3D matrix in cpp
mincpp1 | Search for the min values of 2D matrix in cpp
normalizeSensitivity | Normalize the drug sensitivity data
searchSpace | Generate search space
sffs | SFFS switch function
sffsBinary | Model selection with sffs for the binary drug-target interaction data
sffsBinary1 | Model selection with sffs for the binary drug-target interaction data using two.sided TIMMA model
sffsBinary2 | Model selection with filtered binary drug-target interaction data
sffsCategory | Model selection with sffs for the multi-class drug-target interaction data using one.sided TIMMA model
sffsCategory1 | Model selection with sffs for the multi-class drug-target interaction data using two.sided TIMMA model
sffsCategoryWeighted | Model selection with sffs for the multi-class drug-target interaction data using one.sided and weighted TIMMA model
sffsCategoryWeighted1 | Model selection with sffs for the multi-class drug-target interaction data using two.sided and weighted TIMMA model
sumcpp | Sum for 3D matrix
sumcpp1 | Sum for 2D matrix in cpp
targetRank | Generate the list of ranked target combinations
TIMMA | Target Inhibition inference using Maximization and Minimization Averaging
timma | Main function for the timma package
timmaBinary | Predicting drug sensitivity with binary drug-target interaction data
timmaBinary1 | Predicting drug sensitivity with binary drug-target interaction data using modified maximization and minimization rules
timmaCategory | Predicting drug sensitivity with multi-class drug-target interaction data using one.sided TIMMA model
timmaCategory1 | Predicting drug sensitivity with multi-class drug-target interaction data using two.sided TIMMA model
timmaCategoryWeighted | Predicting drug sensitivity with multi-class drug-target interaction data using one.sided and weighted TIMMA model
timmaCategoryWeighted1 | Predicting drug sensitivity with multi-class drug-target interaction data using two.sided and weighted TIMMA model
timmaModel | Predicting drug sensitivity with binary drug-target interaction data
timmaModel1 | Predicting drug sensitivity with binary drug-target interaction data using two.sided TIMMA model
timmaSearchBinary | Prediction in the search space with one.sided TIMMA model
timmaSearchBinary1 | Prediction in the search space with two.sided TIMMA model
tyner_interaction_binary | A binary drug-target interaction data
tyner_interaction_multiclass | A multi-class drug-target interaction data
tyner_sensitivity | The drug sensitivity data