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 |