alteredExpressionGroupSet {alteredExpression}R Documentation

alteredExpressionGroupSet

Description

Algorithm to find in a genome-wide expression dataset (usually obtained with microarrays) the set of groups of genes which presents the most variable or altered figures in their expression profiles when comparing a control set (i.e. control samples) versus a query set (i.e. disease or altered samples). It searchs for consecutive groups with decreasing variability.

Usage

alteredExpressionGroupSet(A.data.frame, length.1, maxiter=500, initialSize = 20, vSize = 0.5, pctSubset = 0.1, filMed = 0, numGroups = 7, maxnull = 20)

Arguments

A.data.frame Two-dimensional data frame with samples (subjects, arrays) as columns and genes (genes, gene probes) as rows.
length.1 Number of columns in the data frame that correspond to control samples (placing the controls always at the beginning, starting with column 1).
maxiter Maximum number of iterations allowed to find one group. A value of 500 iterations is set up by default.
initialSize Number of genes included in the group for the initial random sampling of the dataset. A value of 20 genes is set up by default.
vSize Parameter to modulate or variate the effect of the group size. It can vary between 0 and 1, being close to 0 for higher size effect and close to 1 for lower size effect. The vSize is fixed to 0.5 by default.
pctSubset Parameter, varying between 0 and 1, that fix the percentage of in-out genes (ioGenes) that are randomly selected and changed every time the algorithm iterates. A value of 0.1 (10pct) is set up by default.
filMed Means prefilter between control and altered samples. This parameter excludes from the analysis the input genes that do not present a minimal change in mean expression.
numGroups Maximum number of groups generated by the algorithm. It is fixed to 7 by default.
maxnull Maximum number of times that the algorithm allows that the resulting group is null before stopping. It is fixed to 20 by default.

Details

See references for further details.

Value

alteredSet An object of class alteredSet.

Author(s)

Prieto C, Rivas MJ, Sanchez JM, Lopez-fidalgo J and De Las Rivas J email:jrivas@usal.es,http://bioinfow.dep.usal.es

References

Prieto C, Rivas MJ, Sanchez JM, Lopez-fidalgo J and De Las Rivas J (2005) Algorithm to find gene expression profiles of differential deregulation and identify families of disease-altered genes. Bioinformatics (PMID: 16500942) http://bioinfow.dep.usal.es/AlteredExpression.

See Also

alteredExpressionGroup,altered,alteredset

Examples

 # 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)


[Package alteredExpression version 1.0 Index]