DFP: Gene Selection

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This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.

Author
R. Alvarez-Gonzalez, D. Glez-Pena, F. Diaz, F. Fdez-Riverola
Date of publication
None
Maintainer
Rodrigo Alvarez-Glez <rodrigo.djv@uvigo.es>
License
GPL-2
Version
1.32.0

View on Bioconductor

Man pages

calculateDiscriminantFuzzyPattern
Calculates the Discriminant Fuzzy Pattern to select...
calculateFuzzyPatterns
Calculates a Fuzzy Pattern for each category of the samples
calculateMembershipFunctions
Calculates Membership Functions
DFP-internal
Internal DFP objects
DFP-package
DFP Package Overview
discretizeExpressionValues
Function to discretize gene expression data
discriminantFuzzyPattern
Discriminant Fuzzy Pattern to filter genes
ExpressionLevel-class
Class "ExpressionLevel"
HighExpressionLevel-class
Class "HighExpressionLevel"
LowExpressionLevel-class
Class "LowExpressionLevel"
MediumExpressionLevel-class
Class "MediumExpressionLevel"
plotDiscriminantFuzzyPattern
Plots the Discriminant Fuzzy Pattern of the relevant genes
plotMembershipFunctions
Plots the Membership Functions (Low, Medium, High) used to...
readCSV
Creates an ExpressionSet with an AnnotatedDataFrame from CSV...
rmadataset
A sample ExpressionSet object
showDiscreteValues
Prints the labels to which the algorithm converts the gene...
showFuzzyPatterns
Plots the Fuzzy Patterns corresponding to a class
show-methods
Prints the slots (attributes) of an ExpressionLevel object

Files in this package

DFP/DESCRIPTION
DFP/NAMESPACE
DFP/R
DFP/R/AllClasses.R
DFP/R/DFP.R
DFP/R/show-methods.R
DFP/build
DFP/build/vignette.rds
DFP/data
DFP/data/rmadataset.rda
DFP/inst
DFP/inst/doc
DFP/inst/doc/DFP.R
DFP/inst/doc/DFP.Rnw
DFP/inst/doc/DFP.pdf
DFP/inst/extdata
DFP/inst/extdata/exprsData.csv
DFP/inst/extdata/pData.csv
DFP/man
DFP/man/DFP-internal.Rd
DFP/man/DFP-package.Rd
DFP/man/ExpressionLevel-class.Rd
DFP/man/HighExpressionLevel-class.Rd
DFP/man/LowExpressionLevel-class.Rd
DFP/man/MediumExpressionLevel-class.Rd
DFP/man/calculateDiscriminantFuzzyPattern.Rd
DFP/man/calculateFuzzyPatterns.Rd
DFP/man/calculateMembershipFunctions.Rd
DFP/man/discretizeExpressionValues.Rd
DFP/man/discriminantFuzzyPattern.Rd
DFP/man/plotDiscriminantFuzzyPattern.Rd
DFP/man/plotMembershipFunctions.Rd
DFP/man/readCSV.Rd
DFP/man/rmadataset.Rd
DFP/man/show-methods.Rd
DFP/man/showDiscreteValues.Rd
DFP/man/showFuzzyPatterns.Rd
DFP/vignettes
DFP/vignettes/DFP.Rnw