filterGenesets: Filtering of gene sets

In GiANT: Gene Set Uncertainty in Enrichment Analysis

Description

Filters gene sets according to different criteria.

Usage

filterGeneSets(
	geneSets,
	includedGenes = NULL,
	minIntersectSize = length(includedGenes),
	adjMatrix = NULL,
	steps = NULL)

Arguments

geneSets	A list of gene sets, where each gene set is a vector of gene names corresponding to the row names of dat.
includedGenes	A vector of gene names whose occurence in each of the gene sets is checked. The further parameters how these genes are used to filter gene sets
minIntersectSize	If this parameter is not NULL, only gene sets with an intersection of at least minIntersectSize genes with respect to includedGenes (or includedGenes expanded by its interactions if adjMatrix and steps are supplied) are included in the result set. By default, this is the size of includedGenes, requiring includedGenes to be a subset of each gene set.
adjMatrix	An optional adjacency matrix in which an entry is 1 if there is a direct interaction between the corresponding genes and 0 otherwise. If this is non-null, the set of genes in includedGenes is expanded by adding all genes whose distance in the adjacency graph is at most steps.
steps	The maximum distance of interacting genes to the genes in includedGenes according to adjMatrix to be added to the expanded gene list. E.g., steps = 1 means that all genes which are direct interaction partners of the initial genes in includedGenes are added to includedGenes.

Value

Returns a filtered list of gene sets with the same structure as geneSets.

See Also

geneSetAnalysis, preprocessGs

Examples

geneSets <- list(
		gs1 = paste("gene",1:20,sep=""),
		gs2 = paste("gene",50:60,sep=""),
		gs3 = paste("gene",90:92,sep=""),
		gs4 = paste("gene",55:65,sep="")
	)

newGeneSets1 <- filterGeneSets(
	geneSets = geneSets,
	includedGenes = c("gene55","gene60"))

newGeneSets2 <- filterGeneSets(
	geneSets = geneSets,
	includedGenes = c("gene1","gene55","gene20","gene100"),
	minIntersectSize = 2)

examplePathway <- c("gene1","gene2","gene3","gene4")
pathwayAdjMatrix <- matrix(0,100,100)
rownames(pathwayAdjMatrix) <- paste("gene",1:100,sep="")
colnames(pathwayAdjMatrix) <- paste("gene",1:100,sep="")

# gene1 interacts with gene2 and gene3
# -> step 1 if gene1 is starting point
pathwayAdjMatrix[1,2:3] <- 1
pathwayAdjMatrix[2:3,1] <- 1

# gene3 interacts with gene4
# -> step 2 if gene1 is starting point
pathwayAdjMatrix[3,4] <- 1
pathwayAdjMatrix[4,3] <- 1

newGeneSets3 <- filterGeneSets(
	geneSets = geneSets,
	includedGenes = "gene1",
	adjMatrix = pathwayAdjMatrix,
	steps = 2)

GiANT documentation built on Oct. 23, 2020, 7:56 p.m.