tspair (version 1.30.0)

ts.pair: Calculation of top scoring pairs.

Description

This function calculates the pair of genes that show the maximum difference in ranking between two user specified groups. The function tspcalc() is the general version of this function that accepts eSets.

Usage

ts.pair(dat,grp)

Arguments

dat

An m genes by n arrays matrix of expression data.

grp

A group indicator with values 0 and 1 for the two groups.

Value

A tsp object with elements:

index

A two-column matrix where each row is a pair of indices from the data matrix achieving the top score

tspscore

The rank based score described in Geman et al. (2004), essentially the empirical average of sensitivity and specificity for the pair.

score

The tie-breaking score described in Tan et al. (2005).

grp

The binary group indicator.

tspdat

Row i and row (i + Number of total TSPs) of this data matrix represent the expression data for the ith TSP pair.

labels

The group labels for the two groups as defined by the grp variable.

Details

ts.pair() only works for two group classification. All the caveats for tspcalc() apply here, but this function only works for matrix and vector arguments, for a more general function see tspcalc(). The top scoring pairs methodology was originally described in Geman et al. (2004). and the unique TSP idea was described in Tan et al. (2005).

References

D. Geman, C. d'Avignon, D. Naiman and R. Winslow, "Classifying gene expression profiles from pairwise mRNA comparisons," Statist. Appl. in Genetics and Molecular Biology, 3, 2004.

A.C. Tan, D.Q. Naiman, L. Xu, R.L. Winslow, D. Geman, "Simple decision rules for classifying human cancers from gene expression profiles," Bioinformatics, 21: 3896-3904, 2005.

See Also

tspplot, tspcalc, tspsig,predict.tsp, summary.tsp

Examples

  ## Not run: 
#   ## Load data
#   data(tspdata) 
#   tsp1 <- ts.pair(dat,grp)
#   tsp1$index
#  ## End(Not run)