predict.tsp: Prediction based on a tsp object

In tspair: Top Scoring Pairs for Microarray Classification

Description

This function can be used to predict outcome values for a data set based on a tsp object.

Usage

  ## S3 method for class 'tsp'
predict(object,dat=NULL,select=NULL,...)

Arguments

object	A tsp object
dat	Can take two values: (a) an m genes by n arrays matrix of expression data or (b) an eSet object
select	An indicator of which TSP to use,defaults to the first TSP.
...	Plotting arguments (ignored)

Details

predict() accepts a tsp object calculated on an expression set or gene expression matrix. If no other data set is included, the tsp predictions for the original data set are produced. If a second gene expression matrix or expression set is included, predict() looks for the gene names of the TSP in tspobj and attempts to match them in the rownames or featureNames of the gene expression matrix. If rownames or featureNames are not available, the prediction is based on the row numbers. If a match is identified, predict() makes a prediction for each gene based on the output.

Value

predict

A class prediction for each array of dat based on the TSP from tspobj

Author(s)

Jeffrey T. Leek [e-mail]

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,ts.pair, tspcalc,tspsig,summary.tsp

Examples

  ## Not run: 
  ## Load data
  data(tspdata) 

  ## Run tspcalc() on a data matrix and grp vector
  tsp1 <- tspcalc(dat,grp)

  ## Get predictions for a new eSet or data matrix
  predict.tsp(tsp1,dat2,1)
  predict(tsp1,eSet2,1)
 
## End(Not run)

tspair documentation built on Nov. 8, 2020, 6:51 p.m.