ktspplot: Graphical representation of ktsp objects

In ktspair: k-Top Scoring Pairs for Microarray Classification

Description

Show a graphical representation of ktsp objects based on the expressions of the genes present in the pairs constituting the k-TSP.

Usage

ktspplot(ktspobj, select = NULL)

Arguments

ktspobj	A ktsp object (computed through the functions ktspcalc or kts.pair).
select	If the number of TSPs in the k-TSP is greater than 1, one can choose the representation of a single TSP (select = 1,2,...,k). By default the graphical representation of every TSPs in succession is ploted.

Details

ktspplot() creates a two dimensional graph for a single TSP present in the k-TSP. The graph plots the expression of the first gene in the pair versus the expression of the second gene in the pair of interest. The group of the observations are ploted in red and blue, the score of the current pair is shown on the top of the graph. The black line of slope 1 and intercept 0 represents the decision rule of the current TSP. If not only one TSP is selected, hitting return will plot the next TSP in the k-TSP.

Value

No value is returned. Only a graph is ploted.

Author(s)

Julien Damond [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.

J. Damond, supervised by S. Morgenthaler and S. Hosseinian, "Presentation and study of robustness for several methods to classify individuals based on their gene expressions", Master thesis, Swiss Federal Institute of Technology Lausanne (Switzerland), 2011.

J. Damond, S. Morgenthaler, S. Hosseinian, "The robustness of the TSP and the k-TSP and the computation of ROC curves", paper is submitted in Bioinformatics, December 2011.

Jeffrey T. Leek <[e-mail]> (). tspair: Top Scoring Pairs for Microarray Classification. R package version 1.10.0.

See Also

ktspcalc, kts.pair,predict.ktsp, summary.ktsp

Examples

  ## Not run: 
  ## Load data
  data(ktspdata) 
  ktsp <- ktspcalc(dat,grp,3)
  ktspplot(ktsp,select=1)
  ktspplot(ktsp)
 
## End(Not run)

ktspair documentation built on May 2, 2019, 3:25 a.m.