SpeCond: Condition specific detection from expression data

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This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.

Author
Florence Cavalli
Date of publication
None
Maintainer
Florence Cavalli <florence@ebi.ac.uk>
License
LGPL (>=2)
Version
1.28.0

View on Bioconductor

Man pages

createParameterMatrix
Create or Modify the SpeCond argument parameters
expressionSpeCondExample
The expression matrix example used in the SpeCond package
expSetSpeCondExample
An ExpressionSet example object used in the SpeCond package
fitNoPriorWithExclusion
Fit the expression values profile with a mixture of normal...
fitPrior
Fit the expression value profiles with a mixture of normal...
getDefaultParameter
Get the default parameter to use SpeCond function
getFullHtmlSpeCondResult
Visualisation function of the SpeCond analysis results
getGeneHtmlPage
Visualise for each gene the condition-specific detection...
getMatrixFromExpressionSet
Obtain the expression matrix from an ExpressionSet object
getProfile
Create the condition-specific profile of specific matrix...
getSpecificOutliersStep1
Detect the condition-specific as outliers in for the first...
getSpecificResult
Detect the condition-specific genes for the second step on...
simulatedSpeCondData
An example of simulated expression matrix used in the SpeCond...
SpeCond
The condition-specific detection function
writeGeneResult
Write a condition-specific analysis result text file
writeSpeCondResult
Write in text files the main result of the SpeCond function
writeUniqueProfileSpecificResult
Write the specific profiles from the SpeCond analysis

Files in this package

SpeCond/DESCRIPTION
SpeCond/NAMESPACE
SpeCond/R
SpeCond/R/allClass.R
SpeCond/R/fct_SpeCond_2.R
SpeCond/R/fct_SpeCond_visualisation.R
SpeCond/R/show_methods.R
SpeCond/build
SpeCond/build/vignette.rds
SpeCond/data
SpeCond/data/expSetSpeCondExample.rdata
SpeCond/data/expressionSpeCondExample.rdata
SpeCond/data/simulatedSpeCondData.rdata
SpeCond/inst
SpeCond/inst/doc
SpeCond/inst/doc/SpeCond.R
SpeCond/inst/doc/SpeCond.Rnw
SpeCond/inst/doc/SpeCond.pdf
SpeCond/man
SpeCond/man/SpeCond.Rd
SpeCond/man/createParameterMatrix.Rd
SpeCond/man/expSetSpeCondExample.Rd
SpeCond/man/expressionSpeCondExample.Rd
SpeCond/man/fitNoPriorWithExclusion.Rd
SpeCond/man/fitPrior.Rd
SpeCond/man/getDefaultParameter.Rd
SpeCond/man/getFullHtmlSpeCondResult.Rd
SpeCond/man/getGeneHtmlPage.Rd
SpeCond/man/getMatrixFromExpressionSet.Rd
SpeCond/man/getProfile.Rd
SpeCond/man/getSpecificOutliersStep1.Rd
SpeCond/man/getSpecificResult.Rd
SpeCond/man/simulatedSpeCondData.Rd
SpeCond/man/writeGeneResult.Rd
SpeCond/man/writeSpeCondResult.Rd
SpeCond/man/writeUniqueProfileSpecificResult.Rd
SpeCond/vignettes
SpeCond/vignettes/Figure1_null_distribution.png
SpeCond/vignettes/ProcedureSteps.png
SpeCond/vignettes/SpeCond.Rnw