Learn R Programming

SpeCond (version 1.26.0)

Condition specific detection from expression data

Description

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.

Copy Link

Version

Version

1.26.0

License

LGPL (>=2)

Maintainer

Florence Cavalli

Last Published

February 15th, 2017

Functions in SpeCond (1.26.0)

getGeneHtmlPage

Visualise for each gene the condition-specific detection result from SpeCond
getMatrixFromExpressionSet

Obtain the expression matrix from an ExpressionSet object
expressionSpeCondExample

The expression matrix example used in the SpeCond package
getSpecificResult

Detect the condition-specific genes for the second step on the SpeCond procedure
getProfile

Create the condition-specific profile of specific matrix result from SpeCond
writeUniqueProfileSpecificResult

Write the specific profiles from the SpeCond analysis
writeGeneResult

Write a condition-specific analysis result text file
getSpecificOutliersStep1

Detect the condition-specific as outliers in for the first step on the SpeCond procedure
SpeCond

The condition-specific detection function
createParameterMatrix

Create or Modify the SpeCond argument parameters
fitPrior

Fit the expression value profiles with a mixture of normal components
expSetSpeCondExample

An ExpressionSet example object used in the SpeCond package
simulatedSpeCondData

An example of simulated expression matrix used in the SpeCond package
fitNoPriorWithExclusion

Fit the expression values profile with a mixture of normal components ignoring outliers
getDefaultParameter

Get the default parameter to use SpeCond function
getFullHtmlSpeCondResult

Visualisation function of the SpeCond analysis results
writeSpeCondResult

Write in text files the main result of the SpeCond function