Package: DFP 1.70.0

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

DFP_1.70.0.tar.gz
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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-release.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 4 scripts 544 downloads 3 mentions 11 exports 3 dependencies

Last updated from:361292aca6 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	114
linux-devel	NOTE	138
source / vignettes	OK	167
linux-release	NOTE	206
macos-release	NOTE	99
macos-oldrel	NOTE	97
windows-devel	NOTE	79
windows-release	NOTE	64
windows-oldrel	NOTE	81
wasm-release	OK	79

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