SpeCond: Condition specific detection from expression data
Version 1.30.0

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.

AuthorFlorence Cavalli
Bioconductor views Clustering DifferentialExpression Microarray MultipleComparison ReportWriting
Date of publicationNone
MaintainerFlorence Cavalli <florence@ebi.ac.uk>
LicenseLGPL (>=2)
Version1.30.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SpeCond")

Popular man pages

createParameterMatrix: Create or Modify the SpeCond argument parameters
expressionSpeCondExample: The expression matrix example used in the SpeCond package
getFullHtmlSpeCondResult: Visualisation function of the SpeCond analysis results
getProfile: Create the condition-specific profile of specific matrix...
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
See all...

All man pages Function index File listing

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

Functions

SpeCond Man page Source code
callMclustInStep2 Source code
changeColorClassification Source code
createOutdir Source code
createParameterMatrix Man page Source code
createSingleGeneHtmlPage Source code
detectSpecificFromPV Source code
expSetSpeCondExample Man page
expressionSpeCondExample Man page
fitNoPriorWithExclusion Man page Source code
fitPrior Man page Source code
getDefaultParameter Man page Source code
getDifferenceMedian Source code
getExpressionpatternLegend Source code
getFullHtmlSpeCondResult Man page Source code
getGeneHtmlPage Man page Source code
getHeatmap Source code
getIdenticRow Source code
getLambdaBIC Source code
getListSelectiveResult Source code
getLoglikelihoodFromBIC Source code
getMatrixFromExpressionSet Man page Source code
getMinLoglikelihoodNull Source code
getNullLoglikelihoodRsdMd Source code
getPValueMean Source code
getProfile Man page Source code
getProfileHeatmap Source code
getRsdNull Source code
getScaleMAD Source code
getSelectiveResultTable Source code
getSpecific Source code
getSpecificOutliersStep1 Man page Source code
getSpecificResult Man page Source code
get_normal_separated Source code
mclust_step2 Source code
plotNormalMixture Source code
printHead Source code
printHeadList Source code
printHeadListGene Source code
printHeadMatrix Source code
printHeadVector Source code
show.sp_list Source code
simulatedSpeCondData Man page
writeGeneResult Man page Source code
writeSpeCondResult Man page Source code
writeUniqueProfileSpecificResult Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/allClass.R
R/fct_SpeCond_2.R
R/fct_SpeCond_visualisation.R
R/show_methods.R
build
build/vignette.rds
data
data/expSetSpeCondExample.rdata
data/expressionSpeCondExample.rdata
data/simulatedSpeCondData.rdata
inst
inst/doc
inst/doc/SpeCond.R
inst/doc/SpeCond.Rnw
inst/doc/SpeCond.pdf
man
man/SpeCond.Rd
man/createParameterMatrix.Rd
man/expSetSpeCondExample.Rd
man/expressionSpeCondExample.Rd
man/fitNoPriorWithExclusion.Rd
man/fitPrior.Rd
man/getDefaultParameter.Rd
man/getFullHtmlSpeCondResult.Rd
man/getGeneHtmlPage.Rd
man/getMatrixFromExpressionSet.Rd
man/getProfile.Rd
man/getSpecificOutliersStep1.Rd
man/getSpecificResult.Rd
man/simulatedSpeCondData.Rd
man/writeGeneResult.Rd
man/writeSpeCondResult.Rd
man/writeUniqueProfileSpecificResult.Rd
vignettes
vignettes/Figure1_null_distribution.png
vignettes/ProcedureSteps.png
vignettes/SpeCond.Rnw
SpeCond documentation built on May 20, 2017, 10:23 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.