alteredExpressionGroup {alteredExpression} | R Documentation |
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.
alteredExpressionGroup(A.data.frame, length.1, maxiter = 500, initialSize = 20, vSize = 0.5, pctSubset = 0.1, filMed = 0)
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. |
See references for further details.
altered |
An object of class altered. |
Prieto C, Rivas MJ, Sanchez JM, Lopez-fidalgo J and De Las Rivas J email:jrivas@usal.es,http://bioinfow.dep.usal.es
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.
alteredExpressionGroupSet
,altered
,alteredset
# 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)