SWAP.Calculate.BasicTSPScores {switchBox} | R Documentation |
SWAP.Calculate.BasicTSPScores
calculates basic TSP
scores.
SWAP.Calculate.BasicTSPScores(phenoGroup, inputMat1, inputMat2 = NULL, classes = NULL, RestrictedPairs = NULL, handleTies = FALSE, verbose = FALSE, score_opts=list())
phenoGroup |
is a factor containing the training phenotypes with two levels. |
inputMat1 |
is a numerical matrix containing the measurements (e.g., gene expression data) for choosing the first item of a top scoring pair. |
inputMat2 |
is a numerical matrix containing the
measurements for choosing the second item of a
top scoring pair. If |
classes |
is a character vector of length 2 providing the phenotype class labels (case followed by control). If NULL, the levels of phenoGroup will be taken as the labels. |
RestrictedPairs |
is a character matrix with two columns containing the feature pairs to be considered for score calculations. |
handleTies |
is a logical value indicating whether tie handling should be enabled or not. FALSE by default. |
verbose |
is a logical value indicating whether status messages will be printed or not throughout the function. FALSE by default. |
score_opts |
is a list of additional variables that will be passed on to the scoring function. |
The output is a list containing the following items:
labels |
the levels (phenotypes) in |
score |
is a vector containing the pair-wise scores. |
tieVote |
is a vector indicating the class the pair would vote for in the case of a tie. |
Bahman Afsari bahman.afsari@gmail.com, Luigi Marchionni marchion@jhu.edu, Wikum Dinalankara wdinala1@jhmi.edu
See switchBox for the references.
See SWAP.Calculate.SignedTSPScores
### Load gene expression data for the training set data(trainingData) ### Show group variable for the TRAINING set table(trainingGroup) ### Compute the scores scores = SWAP.Calculate.BasicTSPScores(trainingGroup, matTraining[1:3, ]) # View the scores scores$score