Class alteredset

Description

This is a class representation for alteredExpressionGroup procedure.

Objects from the Class

Objects can be created using the function alteredExpressionGroup.

Slots

set:

Object of class "list" containing the groups of genes as objects generated by alteredExpresionGroupSet procedure.

num:

Object of class "numeric" containing the number of groups generated by alteredExpressionGroupSet procedure.

Methods

getAltered

signature(alteredset = "alteredset", index = "numeric"): Get the group generated in the index position.

getAlteredGenes

signature(alteredset = "alteredset", index = "numeric"): Get the list of genes generated in the index position.

getFscore

altered(alteredset = "alteredset"): Get a vector with the F-score values of all the groups generated.

plotFscore

signature(alteredset = "alteredset"): Generates a plot representing the F-score values of all the groups generated.

orderAlteredSet

signature(alteredset = "alteredset"): Generates an alteredset ordered by F-score.

alteredset2html

signature(alteredset = "alteredset", filename = "character", plotExprs = "logical", plotScal = "logical"): Generate a HTML file representing the set of groups obtained.
filename - is the name of the file.
plotExprs - includes for each group the expression plot in the html file.
plotScal - includes for each group the scaled-plot in the html file.

show

signature(altered = "altered"): Shows the output of the alteredExpressionGroupSet analysis.

Author(s)

Prieto C, Rivas MJ, Sanchez JM, Lopez-fidalgo J and De Las Rivas J email:jrivas@usal.es or cprieto@usal.es

References

Prieto C, Rivas MJ, Sanchez JM, Lopez-fidalgo J and De Las Rivas J (2006) Algorithm to find gene expression profiles of differential deregulation and identify families of disease-altered genes. Bioinformatics (PMID: 16500942)

See Also

alteredExpressionGroup,alteredExpressionGroupSet,altered,

Examples

## Not run: 
 # Generates the data for the example
 data <- as.data.frame(rbind(cbind(matrix(rep(5:9,120) + rnorm(600,mean=0,sd=0.2),ncol=6,byrow=TRUE),matrix(sample(1:15,1000,replace=TRUE),ncol=10)),matrix(sample(1:15,3200,replace=TRUE),ncol=16)))
 # Run the algorithm. This function searchs for three groups
 alteredset <- alteredExpressionGroupSet(data,6,numGroups=3)
 # Get the class of the object
 class(alteredset)
 # Get the gene identifiers of the first group.
 getAlteredGenes(alteredset,1)
 # Get a vector with the F-score values of all the groups generated.
 getFscore(alteredset)
 # Generates a plot representing the F-score values of all the groups generated.
 plotFscore(alteredset)
 # Generates an alteredset ordered by F-score.
 alteredset.order <- orderAlteredSet(alteredset)
 # Generates a plot representing the F-score values of all the groups ordered by F-score.
 plotFscore(alteredset.order)
 # Get the group generated in the first position.
 altered <- getAltered(alteredset,1)
 # Get the class of the object
 class(altered)
 # Get the expression values of the group
 getExprs(altered)
 # Get the gene identifiers of the group
 getGenes(altered)
 # Generates a group expression plot
 plotExprs(altered)
 # Geterates a group expression scaled-plot
 plotScal(altered)
## End(Not run)