mergeProbesForGenes: Merge multiple probes for one gene

In GiANT: Gene Set Uncertainty in Enrichment Analysis

Merge multiple probes for one gene

Description

Merges all probes belonging to the same gene by identifying duplicate row names in a data matrix.

Usage

mergeProbesForGenes(dat,
	method = c("mean", "max", "min", "median"))

Arguments

dat	A numeric matrix of gene expression values for all analyzed genes. Here, each row corresponds to one probe, and each column corresponds to one sample. The rows must be named with the gene names and may contain duplicates if multiple probes correspond to the same gene.
method	The method which should be used to merge probes entries in dat. Depending on the chosen method, the merged value for a gene and a specific sample is defined as the mean value, the maximum value, the minimum value or the median of all probes of this sample belonging to the gene.

Value

A matrix of the same structure as dat, but possibly with fewer rows if probes were merged.

See Also

geneSetAnalysis

Examples

dat <- matrix(1:6, nrow=3, ncol=2)
rownames(dat) <- c("g1", "g2", "g1")

newDat <- mergeProbesForGenes(dat, method = "mean")

GiANT documentation built on Sept. 11, 2024, 9:16 p.m.