Application of geneSignature object

Description

The ensembleAdjustable function applies a geneSignature object to a data matrix containing expression values and gene symbols or an ExpressionSet object.

Usage

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ensembleAdjustable(dataSet, geneSig, index=F)

Arguments

dataSet

data set object, may be numeric matrix or an ExpressionSet

geneSig

geneSignature object containing directions, thresholds, and gene symbols

index

index to indicate which samples are to be subsetted, may be FALSE for no subsetting or a vector of column numbers

Value

A logical vector with length equal to the number of samples (or samples subsetted), TRUE indicating a positive, FALSE indicating a negative

Author(s)

UnJin Lee

Examples

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require(Biobase)
## Generate test geneSignature object with 0s for thresholds
gs <- setGeneSignature(g=new("geneSignature"), direct=c(1,1,1), genes=c("A", "B", "C"), thresholds=c(0, 0, 0))

## Generate randomly distributed matrix and ExpressionSet
mat <- matrix(rnorm(9, 0, 1), nrow=3)
rownames(mat) <- c("A", "B", "C")
posmat <- abs(mat)
expset <- new("ExpressionSet", exprs=mat)

## Apply geneSignature to matrices
ensembleAdjustable(mat, gs)
ensembleAdjustable(posmat, gs)

## Apply geneSignature to ExpressionSet
ensembleAdjustable(expset, gs)

## Apply geneSignature with subsetting
ensembleAdjustable(mat, gs, c(1, 3))
ensembleAdjustable(expset, gs, c(1, 3))