Package: DFP 1.71.0

Rodrigo Alvarez-Glez

DFP: Gene Selection

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.

Authors:R. Alvarez-Gonzalez, D. Glez-Pena, F. Diaz, F. Fdez-Riverola

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DFP/json (API)

# Install 'DFP' in R:

install.packages('DFP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

rmadataset - A sample ExpressionSet object

On BioConductor:DFP-1.71.0(bioc 3.24)DFP-1.70.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray differentialexpression

3.78 score 5 scripts 3 mentions 11 exports 3 dependencies

Last updated from:f4abc96fcd. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	186
linux-devel-x86_64	NOTE	137
source / vignettes	OK	214
linux-release-x86_64	NOTE	183
macos-release-arm64	NOTE	97
macos-oldrel-arm64	NOTE	73
windows-devel	NOTE	66
windows-release	NOTE	80
windows-oldrel	NOTE	89
wasm-release	OK	92

Exports:calculateDiscriminantFuzzyPattern calculateFuzzyPatterns calculateMembershipFunctions discretizeExpressionValues discriminantFuzzyPattern plotDiscriminantFuzzyPattern plotMembershipFunctions readCSV show showDiscreteValues showFuzzyPatterns

Dependencies:Biobase BiocGenerics generics

Howto: Discriminat Fuzzy Pattern

Rendered fromDFP.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

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