alteredExpressionGroup {alteredExpression}R Documentation

alteredExpressionGroup

Description

Algorithm to find in a genome-wide expression dataset (usually obtained with microarrays) the group 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 just for ONE group.

Usage

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

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.

Details

See references for further details.

Value

altered An object of class altered.

Note

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

alteredExpressionGroupSet,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 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)

[Package alteredExpression version 1.0 Index]