altered {alteredExpression}R Documentation

Class altered

Description

This is a class representation for alteredExpressionGroup procedure.

Objects from the Class

Objects can be created using the function alteredExpressionGroup.

Slots

exprs:
Object of class "data.frame" containing the expression values of the resulting group of genes.
fscore:
Object of class "numeric" representing the expected F-score (statistical parameter) of this group of genes
rrv:
Object of class "numeric" containing the Residual Relative Variance (RRV) of this group of genes.
len:
Object of class "numeric" containing he number of control samples. The control samples have to be placed as the initial columns in the expresion matrix.
iter:
Object of class "numeric" representing the number of iterations done by the algorithm to find the group.
vsize:
Object of class "numeric" representing the value used to modulate or variate the effect of the group size.
pctsubset:
Object of class "numeric" containing the percentage of in-out genes that is changed in each iteration.
filmed:
Object of class "numeric" containing the value of the prefilter used, that corresponds to a certain difference in the mean expression value of the control samples versus the mean expression value of the altered samples.

Methods

getExprs
signature(altered = "altered"): Get the expression values of the group.
getGenes
signature(altered = "altered"): Get the gene identifiers of the group.
plotExprs
altered(altered = "altered"): Generates a group expression plot.
plotScal
signature(altered = "altered"): Generates a group expression scaled-plot, scaling all the values by making 1 the gene expression values of the first sample.
altered2html
signature(altered = "altered", filename = "character", plotExprs = "logical", plotScal = "logical"): Generates a HTML file representing the group.
filename - is the name of the file.
plotExprs - includes the group expression plot in the html file.
plotScal - includes the group expression scaled-plot in the html file.
show
signature(altered = "altered"): Shows the output of the alteredExpressionGroup 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,alteredSet

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 just for one group
 altered <- alteredExpressionGroup(data,6)
 # 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)

[Package alteredExpression version 1.0 Index]