altered {alteredExpression} | R Documentation |
This is a class representation for alteredExpressionGroup procedure.
Objects can be created using the function alteredExpressionGroup
.
exprs
:"data.frame"
containing
the expression values of the resulting group of genes.fscore
:"numeric"
representing
the expected F-score (statistical parameter) of this group of genesrrv
:"numeric"
containing
the Residual Relative Variance (RRV) of this group of genes.len
:"numeric"
containing
he number of control samples. The control samples have to be
placed as the initial columns in the expresion matrix.iter
:"numeric"
representing
the number of iterations done by the algorithm to find the group. vsize
:"numeric"
representing
the value used to modulate or variate the effect of the group size.pctsubset
:"numeric"
containing
the percentage of in-out genes that is changed in each iteration.filmed
:"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.signature(altered = "altered")
: Get the expression values of the group.signature(altered = "altered")
: Get the gene identifiers of the group.altered(altered = "altered")
: Generates a group expression plot.signature(altered = "altered")
: Generates a group expression scaled-plot,
scaling all the values by making 1 the gene expression values of the first sample.signature(altered = "altered", filename = "character", plotExprs = "logical",
plotScal = "logical")
: Generates a HTML file representing the group.signature(altered = "altered")
: Shows the output of the alteredExpressionGroup
analysis.Prieto C, Rivas MJ, Sanchez JM, Lopez-fidalgo J and De Las Rivas J email:jrivas@usal.es or cprieto@usal.es
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)
alteredExpressionGroup
,alteredExpressionGroupSet
,alteredSet
## 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)