ktspair (version 1.0)

bootstrap.graphic.ktsp: Graphical display of the bootstrap procedure

Description

This function displays the results of the bootstrap obtained with the function bootstrap(). It plots the frequency of appearance of the single genes as well as the pairs. If k was not set by the used an histogram of the values of k is also ploted.

Usage

bootstrap.graphic.ktsp(bootstrap, para1 = 0, para2 = 0, title = NULL, mtext = NULL)

Arguments

bootstrap

A boostrap object obtained with the function bootstrap().

para1

This parameter allows the user to control the lower bound of the frequency of appearance of the genes (the first plot).

para2

This parameter allows the user to control the lower bound of the frequency of appearance of pairs of the genes (the second plot).

title

This is used to determine the title of the graph.

mtext

Allow the user to specify a subtitle.

Value

None, a graphic is ploted.

Details

The pair(s) of genes with the red dot represent(s) the pair(s) obtained on the original dataset.

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 (). tspair: Top Scoring Pairs for Microarray Classification. R package version 1.10.0.

See Also

ktspcalc, ktspplot,predict.ktsp, summary.ktsp

Examples

  ## Not run: 
#   ## Load data
#    data(ktspdata)
#    bootstrap1 <- bootstrap(dat, grp, k=3, n=20)
#    bootstrap2 <- bootstrap(dat, grp, n=30, seed=1)
#    bootstrap.graphic.ktsp(bootstrap1)
#    bootstrap.graphic.ktsp(bootstrap2)   
#   ## End(Not run)