ktspair: k-Top Scoring Pairs for Microarray Classification

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These functions compute the k best pairs of genes used to classify samples based on the relative rank of the genes expression within each profile. A score based on the sensitivity and the specificity is calculated for every possible pair. The k pairs with the highest score will be selected with the restriction that a gene can appear in at most one pair. The value of k is either set as a parameter chosen by the user or computed through crossvalidation. Other functions related to the k-TSP are also available, for example the functions prediction, summary, plot, etc. can be found in the package.

Author
Julien Damond <julien.damond@gmail.com>
Date of publication
2011-12-23 10:06:13
Maintainer
Julien Damond <julien.damond@gmail.com>
License
GPL-2
Version
1.0

View on CRAN

Man pages

AUC.calc
Compute the AUC
bootstrap.graphic.ktsp
Graphical display of the bootstrap procedure
bootstrap.ktsp
Bootstrap procedure for the k-TSP
cv
Crossvalidation for the parameter k
cv2
Crossvalidation with chosen pairs of genes
dat
Simulated gene expressions of individuals.
eSet
Simulated gene expressions of individuals.
grp
Group of the individuals.
kts.pair
Calculation of the k top scoring pairs.
ktspair-package
Computation of the k-TSP
ktspcalc
Compute the k top scoring pairs based on a gene expression...
ktspcalc2
The k-TSP with chosen pairs of genes
ktspdata
Simulated dataset of gene expressions in a matrix form.
ktspplot
Graphical representation of ktsp objects
make.consecutive.int
Transform the group vector into a binary vector
ordertsp
Ordering of the pairs of genes
plot.ktsp
Graphical representation of ktsp objects
predict.ktsp
Prediction using a ktsp object
print.ktsp
Print the results of the k-TSP
rank_na
Rank the gene expression and Replace NA
ROC.graphic.ktsp
Graphical display of the ROC curve
ROC.offset
ROC curve based on the offset method for k-TSP method
ROC.voting
ROC curve based on the voting system for k-TSP method
summary.ktsp
Summary of ktsp object

Files in this package

ktspair
ktspair/MD5
ktspair/src
ktspair/src/ktsp.cc
ktspair/R
ktspair/R/summary.ktsp.r
ktspair/R/ROC.voting.r
ktspair/R/ROC.offset.r
ktspair/R/ROC.graphic.ktsp.r
ktspair/R/rank_na.r
ktspair/R/print.ktsp.r
ktspair/R/predict.ktsp.r
ktspair/R/plot.ktsp.r
ktspair/R/ordertsp.r
ktspair/R/make.consecutive.int.r
ktspair/R/ktspplot.r
ktspair/R/ktspcalc2.r
ktspair/R/ktspcalc.r
ktspair/R/kts.pair.r
ktspair/R/cv2.r
ktspair/R/cv.r
ktspair/R/bootstrap.ktsp.r
ktspair/R/bootstrap.graphic.ktsp.r
ktspair/R/AUC.calc.r
ktspair/NAMESPACE
ktspair/man
ktspair/man/summary.ktsp.Rd
ktspair/man/ROC.voting.Rd
ktspair/man/ROC.offset.Rd
ktspair/man/ROC.graphic.ktsp.Rd
ktspair/man/rank_na.Rd
ktspair/man/print.ktsp.Rd
ktspair/man/predict.ktsp.Rd
ktspair/man/plot.ktsp.Rd
ktspair/man/ordertsp.Rd
ktspair/man/make.consecutive.int.Rd
ktspair/man/ktspplot.Rd
ktspair/man/ktspdata.Rd
ktspair/man/ktspcalc2.Rd
ktspair/man/ktspcalc.Rd
ktspair/man/ktspair-package.Rd
ktspair/man/kts.pair.Rd
ktspair/man/grp.Rd
ktspair/man/eSet.Rd
ktspair/man/dat.Rd
ktspair/man/cv2.Rd
ktspair/man/cv.Rd
ktspair/man/bootstrap.ktsp.Rd
ktspair/man/bootstrap.graphic.ktsp.Rd
ktspair/man/AUC.calc.Rd
ktspair/inst
ktspair/inst/doc
ktspair/inst/doc/ktspair-manual.pdf
ktspair/inst/doc/.fr-hy2VZf
ktspair/inst/doc/.fr-hy2VZf/ktspairextend
ktspair/inst/doc/.fr-hy2VZf/ktspairextend/inst
ktspair/inst/doc/.fr-hy2VZf/ktspairextend/inst/doc
ktspair/inst/doc/.fr-hy2VZf/ktspairextend/inst/doc/ktspair-manual.pdf
ktspair/INDEX
ktspair/DESCRIPTION
ktspair/demo
ktspair/demo/ktspair.r
ktspair/demo/00Index
ktspair/data
ktspair/data/ktspdata.RData
ktspair/.Rbuildindex.9995
ktspair/.Rbuildindex.31678
ktspair/.Rbuildindex.31551
ktspair/.Rbuildindex.10034