SWAP.Calculate.SignedTSPScores: Function to calculate signed TSP scores.

In marchion/switchBox: Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

Description

SWAP.Calculate.SignedTSPScores calculates signed TSP scores. The input provided to this function should be already sanitized; to filter features and calculate pairwise scores, use SWAP.CalculateScores instead.

Usage

SWAP.Calculate.SignedTSPScores(phenoGroup, inputMat1, 
  inputMat2 = NULL, classes = NULL, RestrictedPairs = NULL, 
    handleTies = FALSE, verbose = FALSE, score_opts=list())

Arguments

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 NULL, inputMat1 will be used for this.
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.

Value

The output is a list containing the following items:

labels	the levels (phenotypes) in phenoGroup.
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.

Author(s)

Bahman Afsari [e-mail], Luigi Marchionni [e-mail], Wikum Dinalankara [e-mail]

References

See switchBox for the references.

See Also

See SWAP.Calculate.BasicTSPScores

Examples

### 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.SignedTSPScores(trainingGroup, matTraining[1:3, ])

# View the scores
scores$score

marchion/switchBox documentation built on May 9, 2019, 4:07 p.m.