ensembleAdjustable: Application of geneSignature object

In sigsquared: Gene signature generation for functionally validated signaling pathways

Description

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

Usage

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

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))

sigsquared documentation built on Nov. 8, 2020, 6:59 p.m.