label_prop_gsea: Over-representaion analysis with the label propagation...

In gsean: Gene Set Enrichment Analysis with Networks

Description

ORA is performed by GSEA with the label propagation algorithm

Usage

label_prop_gsea(geneset, x, adjacency, threshold = 0.99, nperm = 1000,
                minSize = 1, maxSize = Inf, gseaParam = 1, nproc = 0,
                BPPARAM = NULL, ...)

Arguments

geneset	list of gene sets
x	set of genes
adjacency	adjacency matrix
threshold	threshold of correlation for nodes to be considered neighbors (default: 0.99)
nperm	number of permutations (default: 1000)
minSize	minimal size of a gene set (default: 1)
maxSize	maximal size of a gene set (default: Inf)
gseaParam	GSEA parameter value (default: 1)
nproc	see fgsea::fgsea
BPPARAM	see fgsea::fgsea
...	additional parameters for label propagation; see RANKS::label.prop

Value

GSEA result

Author(s)

Dongmin Jung

See Also

fgsea::fgsea, RANKS::label.prop

Examples

data(examplePathways)
data(exampleRanks)
exampleRanks <- exampleRanks[1:100]
geneNames <- names(exampleRanks)
set.seed(1)
x <- sample(geneNames, 10)
adjacency <- diag(length(exampleRanks))
rownames(adjacency) <- geneNames
result.GSEA <- label_prop_gsea(examplePathways, x, adjacency)

gsean documentation built on Nov. 8, 2020, 6:36 p.m.