SWAP.Calculate.BasicTSPScores: Function to calculate basic TSP scores.

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/exportedFuncs.R

Description

SWAP.Calculate.BasicTSPScores calculates basic TSP scores.

Usage

1
2
3
SWAP.Calculate.BasicTSPScores(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 [email protected], Luigi Marchionni [email protected], Wikum Dinalankara [email protected]

References

See switchBox for the references.

See Also

See SWAP.Calculate.SignedTSPScores

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
### 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

switchBox documentation built on Nov. 1, 2018, 2:46 a.m.