alteredset {alteredExpression} | R Documentation |
This is a class representation for alteredExpressionGroup procedure.
Objects can be created using the function alteredExpressionGroup
.
set
:"list"
containing
the groups of genes as objects generated by alteredExpresionGroupSet procedure.num
:"numeric"
containing
the number of groups generated by alteredExpressionGroupSet procedure.signature(alteredset = "alteredset", index = "numeric")
: Get the group generated in the index position.signature(alteredset = "alteredset", index = "numeric")
: Get the list of genes generated in the index position.altered(alteredset = "alteredset")
: Get a vector with the F-score values of all the groups generated.signature(alteredset = "alteredset")
: Generates a plot representing the F-score values of all the groups generated.signature(alteredset = "alteredset")
: Generates an alteredset ordered by F-score.signature(alteredset = "alteredset", filename = "character", plotExprs = "logical",
plotScal = "logical")
: Generate a HTML file representing the set of groups obtained.signature(altered = "altered")
: Shows the output of the alteredExpressionGroupSet 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
,altered
,
## 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 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) ## End(Not run)