Target Inhibition Interaction using Maximization and Minimization Averaging


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Documentation for package ‘timma’ version 1.2.1

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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