tspair: Top Scoring Pairs for Microarray Classification

These functions calculate the pair of genes that show the maximum difference in ranking between two user specified groups. This "top scoring pair" maximizes the average of sensitivity and specificity over all rank based classifiers using a pair of genes in the data set. The advantage of classifying samples based on only the relative rank of a pair of genes is (a) the classifiers are much simpler and often more interpretable than more complicated classification schemes and (b) if arrays can be classified using only a pair of genes, PCR based tests could be used for classification of samples. See the references for the tspcalc() function for references regarding TSP classifiers.

Author
Jeffrey T. Leek <jtleek@jhu.edu>
Date of publication
None
Maintainer
Jeffrey T. Leek <jtleek@jhu.edu>
License
GPL-2
Version
1.32.0

View on Bioconductor

Man pages

dat
Simulated gene expression data.
dat2
Simulated gene expression data.
eSet1
A simulated expression set.
eSet2
A simulated expression set.
grp
A group indicator.
plot.tsp
Graphical display of tsp objects
predict.tsp
Prediction based on a tsp object
summary.tsp
Summary of a tsp object
ts.pair
Calculation of top scoring pairs.
tspcalc
Estimate top scoring pairs from a gene expression matrix
tspdata
Simulated gene expression data in both matrix and expression...
tspplot
Graphical display of tsp objects
tspsig
Significance calculation for top scoring pairs

Files in this package

tspair/DESCRIPTION
tspair/INDEX
tspair/NAMESPACE
tspair/R
tspair/R/tsp.R
tspair/build
tspair/build/vignette.rds
tspair/data
tspair/data/tspdata.rda
tspair/inst
tspair/inst/doc
tspair/inst/doc/tsp.R
tspair/inst/doc/tsp.Rnw
tspair/inst/doc/tsp.pdf
tspair/man
tspair/man/dat.Rd
tspair/man/dat2.Rd
tspair/man/eSet1.Rd
tspair/man/eSet2.Rd
tspair/man/grp.Rd
tspair/man/plot.tsp.Rd
tspair/man/predict.tsp.Rd
tspair/man/summary.tsp.Rd
tspair/man/ts.pair.Rd
tspair/man/tspcalc.Rd
tspair/man/tspdata.Rd
tspair/man/tspplot.Rd
tspair/man/tspsig.Rd
tspair/src
tspair/src/tsp.c
tspair/vignettes
tspair/vignettes/subfigure.sty
tspair/vignettes/tsp.Rnw
tspair/vignettes/tsp.bib
tspair/vignettes/tsp1.pdf
tspair/vignettes/vmargin.sty